The structure and working of the machinery of government rarely corresponds with perfect administrative form. Mind you, apart from the sound common sense of God and the aesthetics of former prime minister Paul Keating, few things get close to perfection. Even William Shakespeare and Piero della Francesca probably had off days.

Thus, it shouldn't be surprising when public or private sector organisations fail sometimes to match the acme of sound management practice.

The inevitable handicaps of departments of state in democratic countries are more awkward than is usual for private companies. In Australia, departments' chief executives (their ministers) are selected from a gene pool formed by the decisions of millions of electors by processes only remotely associated with merit. Ministers are often inexpert in the main functions of their portfolios (cf. Eric Abetz, Joe Hockey, Kevin Andrews, Peter Dutton et al in the current ministry) and they're frequently inexperienced in the management of important or large organisations. Many ministers must learn on the job, and the associated risks and costs are unavoidable consequences of our system of government that are probably worth it.

In addition, the working of the machinery of government can become more fraught when competition between and within political parties is intense. This phenomenon has been grandly on display in recent weeks, as Prime Minister Tony Abbott has tried to juggle cunning strategies to help him cling to his job, with important decisions on national security, replacement submarines and the proper consideration of reports from the Human Rights Commission.

Since declaring that "good government" would kick off more than a year after the Coalition was elected, efforts to help Abbott's survival have disrupted the sound management of his administration. Sure, he's been under the hammer, but it's hard to give him the benefit of the doubt when he has been the principal architect of his misfortunes.

Let's start with the new submarines.

Before the last election, the shadow defence minister, David Johnston, said: "The Coalition ... is committed to building 12 new submarines here in Adelaide." That commitment appears to have been "non-core". Johnston got to the point where he doubted ASC (formerly the Australian Submarine Corporation) could build a canoe, while Abbott warmed to the idea of getting new submarines from Japan.

The government crab-walked away from a pre-election undertaking and left a sour taste on the well-developed palates of the "people of South Australia" and their federal parliamentary representatives. So Abbott tried recently to minimise the loss of South Australian Liberal Party support for him as Prime Minister by calling one of the state's Liberal senators, Sean Edwards, about the submarines. Subsequently, the senator said his constituents should be "hat-throwing" because the government would have a "full and open tender" for the subs.

Alas, Abbott reckons he didn't say that and began talking about a "competitive evaluation process", something Defence Minister Kevin Andrews couldn't explain and which seemed to be news to senior military leaders.

More recently, Andrews announced that France, Germany and Japan had "emerged as potential international partners" in the project. Nevertheless, before a supplier had been identified, Andrews said that whatever happened there would be 500 submarine jobs in South Australia. That should be taken with a grain of salt; it's a rabbit the minister has pulled from his hat.

Replacing the Collins-class submarines is a massive enterprise. It requires the government to decide what it wants the new submarines to do. The Australian National University's professor of defence and strategic studies, Hugh White, says "that question has never been seriously answered". He also points out that the acquisition requires a sophisticated project definition study, the end result of which should be two providers being asked to "submit fully developed tenders for a fixed-price contract". From what is visible, there can be little confidence this is being done. It looks sloppy and it's hard to imagine that recent decisions have gone through a thorough cabinet process.

The picture of good government doesn't get a whole lot better when it comes to the Prime Minister's direction of national security.

While controversial, some of the government's actions against the so-called Islamic State – the deployment of forces in the Middle East, actions against Australians willing to join in the conflict and so on – are respectable in policy terms. On the domestic front, however, Abbott's manoeuvers have been unimpressive.

After the Lindt cafe siege, Abbott and NSW Premier Mike Baird asked their departments' secretaries to inquire into the reasonableness of the actions of government agencies, among other things. This is not be an at-arm's-length inquiry because the Department of the Prime Minister and Cabinet secretary has responsibilities for national security at the Commonwealth level. Moreover, it's impossible to imagine how these two officers could personally conduct a full-blown inquiry while still doing their day jobs. Why is Abbott happy to set up royal commissions to conduct political witch-hunts on pink batts and trade unions but not allow an independent inquiry into the Lindt cafe atrocity? (That's a rhetorical question.)

Then, when two men were arrested in Sydney last month accused of plotting a terrorist act, Abbott detailed the allegations against them in public and said "I don't think it would be possible to witness uglier fanaticism than this". It's to be hoped the Australian Federal Police strongly advised the Prime Minister to keep his mouth shut. If the AFP abetted Abbott, both have prejudiced the prospects of a proper prosecution and a fair trial in what will almost certainly come before a jury. Politicians usually wrongly invoke the sub judice rule to avoid commenting on awkward political matters. In this case, Abbott has abused the rule and made comments he no doubt thinks play to his political advantage.

Enough has already been written about the Prime Minister's national security statement of February 23 and related matters. Much of the commentary has been sound, with Crikey correspondent Bernard Keane's being especially notable. His submission to the joint committee on intelligence and security's inquiry into the proposed data retention legislation (which he comprehensively debunks) should be much more influential that it ultimately may be.

While it is important for Abbott to be able to stand up on national security, it is sufficient here to have a crack at answers to a couple of questions.

Will the belligerent tone of Abbott's recent statement encourage moderate sentiment within the Muslim community, especially it leaders? Probably not and, so far, the signs are not good.

Has he made it likelier that Muslims, especially younger ones, will be less open to radicalisation? Probably not.

Why has he not mentioned the recommendations his review made about better control of firearms? Well, that is sensitive and would require political courage.

Will the "tough Tony" talk bolster Abbott's standing among those who chose him as Prime Minister – i.e. the caucus of Liberal members of Parliament? Maybe not because, apart from any unease about Abbott's tactics, some of his Liberal parliamentary colleagues, who may well have benefited from votes from Muslims at the last election, might not be so lucky next time around.

Whatever the answers to these questions, it's impossible to believe that the responses to some of the recommendations of the joint Commonwealth-state report on the Lindt siege, announced by Abbott on February 23, have gone through an adequate cabinet process as required by the Cabinet Handbook. There just hasn't been the time for that to happen.

Finally, let's come to the government's reception of the Human Rights Commission's report on children in immigration detention centres.

The Attorney-General, George Brandis, wants the commission's president, Professor Gillian Triggs, out of the job because he thinks she's compromised the commission's independence. That's nonsensical and hypocritical and, at the time of writing, the AFP has been asked to investigate whether Brandis should be investigated for offering Triggs an inducement to resign. That's a terrible position for any attorney-general to put himself in. Indeed, as the minister responsible for both the AFP and the Commonwealth Director of Public Prosecutions, Brandis should stand down pending the results of that investigation.

Abbott said the report on children in detention was "a blatantly partisan, politicised exercise and the Human Rights Commission should be ashamed of itself". It would be interesting to know if Abbott read the report before opening his mouth. There are legitimate questions about the timing of the report and its tendentious title (A last resort?) that Triggs has answered adequately. Abbott has produced no evidence to support his strident allegations; they are without foundation and, if shame is to be apportioned, it can be shared between him and Brandis.

Abbott should have said: "Look, we wish the Human Rights Commission could have examined this question earlier, when there were more people in detention centres, and this government has reduced the number of children in them. However, the mistreatment of children is a serious matter and we will consider the commission's recommendations thoroughly and conscientiously, and take whatever action we can to right any wrongs."

Instead, the Prime Minister has recklessly and irresponsibly impugned the integrity of the commission and its staff, presumably because he imagines that will be to his political advantage among those who think that no line can be too firm when it comes to dealing with asylum seekers. And he's sent a clear message to all officials providing advice to the government: if you tell us anything we don't like to hear, you will be cast into exterior darkness and we'll do our best to get rid of you.

And so let us introduce into this unhappy scene the new Public Service Commissioner, John Lloyd. An early test he set for himself was that, if he were to "come across" any unfair criticism, he "would stand up and defend the public service". So, the commissioner was asked if he would stand up and defend the Human Rights Commission. His office replied: "Given Ms Triggs is an independent statutory office holder, not employed under the Public Service Act, the commissioner will not be making any comment."

But hang on: it's not just Triggs who is in the gun. The Prime Minister has undermined the commission's independence and unfairly criticised the commission's staff, who are employed under the Public Service Act.

Under the Lloyd rule, if you happen to be among the thousands of people employed in a public service statutory authority, don't expect the Public Service Commissioner to have the bottle to stick up for you. Presumably, that would also apply to staff in the Public Service Commission, which is headed by an independent statutory office holder: Lloyd.

Lloyd's position is, of course, just too silly for words. In his early days, he's failed one of his own tests and no doubt thereby frustrated the high expectations held for him by my esteemed fellow Informant columnist, J. R. Nethercote. Taken with his disingenuous comments at a recent estimates committee, implying that current public service wage offers are reasonable because they are more or less in line with the anticipated inflation rate for the year ended June 2015, Lloyd is not off to a good start. Putting aside the fact that, in a rational world, inflation rates are irrelevant to fixing pay for public servants, known current wage offers are about half the Reserve Bank's expected inflation for the year ended June 2015. In any event, that's the wrong comparison for Lloyd to have made. He should be looking at the bank's expectations in the period December 2015 to June 2017, when the enterprise bargains are scheduled to operate. In that time, the RBA expects inflation to be between 2 per cent and 3.25 per cent a year.

Since Abbott's belated inauguration of "good government", things have gone from bad to worse and the Prime Minister's scramble to hang on to his job has played a part in that decline. Good policy in the public interest is too often being subordinated to cheap politics. If this is a government of adults, it might be better to put the children in charge.

In the 14th century, Ambrogio Lorenzetti painted a series of allegorical frescoes of good and bad government on the walls of the town hall in the Italian city of Siena. He'd have a field day if he could come to Canberra now.

Paddy Gourley is a former senior public servant, who was deputy secretary of the Defence Department among other roles. [email protected]

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