"Captain Emad", the man alleged to have run a people smuggling operation out of Canberra, left Australia on Tuesday night.

AFP Commissioner Tony Negus told reporters in Canberra today that Captain Emad had not been detained when he left Melbourne, despite an alert going out to authorities.

Mr Negus said there was not enough evidence yet to detain him.

"Yes, it's frustrating," Mr Negus said of the people smuggling case.

But he said the AFP would go ahead with the "full force of the law" in investigating Captain Emad.

Mr Negus said that police had known about the alleged activities of Australian-based people smugglers before they were aired in a Four Corners report on Monday night.

He said the group had been the subject of an investigation for about two years and the investigation was ongoing.

Mr Negus said there were a number of suspects and a number of identities in their investigations into the group.

"There remains insufficient evidence to charge any of the syndicate members at this time," he said.

Four Corners reported that people smuggling agents had come to Australia by boat while posing as asylum seekers and had been granted residency.

The program confronted a man known as "Captain Emad" in the northern Canberra suburb of Gungahlin as he worked collecting supermarket trolleys.

He is alleged to have been involved with another Jakarta-based smuggler, Abu Ali Kuwaiti, a chief organiser for a voyage from Indonesia in which 97 people disappeared and are presumed to have drowned.

It is also claimed Captain Emad had been living in taxpayer-funded housing in Canberra while engaged in people smuggling.

Mr Negus said Four Corners had approached the AFP in February about its people smuggling program and that police had provided the ABC with some information about people smugglers.

He said the AFP did not have ''full visibility" of the program but noted that Four Corners had respected some of the "more sensitive elements" of their investigations.

Mr Negus noted that some of the information presented in the Four Corners report did not amount to evidence that was able to be used in a court of law.

Immigration Minister Chris Bowen has said he has ''no tolerance'' for people gaining refugee status based on false information and the government will investigate claims that people smugglers are based in Australia.

According to the AFP, since September 2008, 14 alleged organisers have been arrested, including five organisers who have been sentenced to up to seven years' jail.

Other alleged organisers are before the court. Four alleged Australian-based organisers were arrested in March 2012.

Labor has been ridiculed by the opposition following the Four Corners report, with Opposition Leader Tony Abbott calling the government ''utterly incompetent'' at border protection.

''If the TV station can find the people smugglers, why can't the government stop them?'' Mr Abbott asked.

Accused People Smuggler Flees Australia