The loss of the boat was never reported and it is alleged the smugglers covered up its disappearance to collect final payments from the passengers' relatives.
Yesterday Bowen said the allegations would be fully investigated and that he had no tolerance for people gaining refugee status based on false information.
"When we have somebody who has been granted refugee status, if it can be established that that status was based on wrong information then that can be revoked," he told ABC radio.
Bowen also defended the "rigorous" screening of asylum seekers, during which about half were rejected at primary assessment for refugee status.
"We do have ASIO doing assessments of people and we do have people who are denied a permanent visa because of their links to people smuggling and their people smuggling activity," he said.
The federal police would not comment on operational matters, but said 14 alleged people smugglers had been arrested since September 2008.
But the Four Corners allegations have refuelled the bitter political controversy over Labor's handling of asylum seekers that began with an easing of the harsh measures of the former Coalition Government, but which have since been steadily toughened.
Since Labor won power in 2007 the number of boats arriving from Indonesia has ballooned.
Last month 1176 asylum seekers arrived - the highest monthly total in more than a decade - and in the first four days of June four boats with 322 people on board were intercepted.
Hundreds of people have died - in addition to earlier tragedies, 200 drowned last December and a further 11 off Malaysia in February. Bowen said 4 per cent of those who attempted the voyage to Australia were estimated to perish at sea.
The Four Corners' allegations of "catastrophic intelligence failings" have added new fuel to the Opposition's campaign to restore the policies of former Liberal Prime Minister John Howard's "Pacific Solution".
The Government wants to process asylum seekers in Malaysia but, despite agreeing to Opposition demands to reopen a former detention centre on Nauru, the Coalition has refused to support new laws unless Labor reintroduces all its former policies.
Four Corners said that early in 2010 Abu Ali al Kuwaiti met other Iraqi smugglers in Jakarta to plan expansion into Australia.
Among them was businessman Captain Emad, also known as Abu Khalid, who was described by an informant as "the head of the snake".
Emad, travelling under the assumed name of Ali al Abassi, was on a boat intercepted near Christmas Island on January 12, 2010.
Within three months he was given a protection visa and, with his wife and family, now lives in Canberra, working as a supermarket trolley collector.
Four Corners said at least six people smugglers were on the same boat, all of whom were also given refugee status.
