Immgration and Border Protection Departmental Secretary Martin Bowles.

No guarantee: Secretary of the Immigration Department, Martin Bowles admitted he could not say for sure if local security contractors who inflicted injuries on detainees during the riots had been stood down. Photo: Andrew Meares

The deadly clashes on Manus Island last week flared after asylum seekers realised the Australian government was ''lying to them'' about plans to resettle them in Papua New Guinea, a migration agent who worked on the island has said.

Liz Thompson, who was helping asylum seekers lodge their refugee applications on Manus Island when the alleged riot broke out, said the asylum seekers launched their protests when a Papua New Guinean official went ''off script'' and acknowledged there were no plans in place for their resettlement.

Her claims came as Australia's top immigration bureaucrat told a Senate hearing that the post-mortem on the body of 23-year-old Reza Barati, who was killed in last Monday's clashes, still had not been carried out.

Martin Bowles, secretary of the Immigration Department, also said he could not guarantee that local security contractors who had inflicted injuries on detainees had been stood down.

The Senate hearing was brought to a dramatic halt late yesterday, when Labor Senator Stephen Conroy accused General Angus Campbell - the commander of the government's Operation Sovereign Borders - of participating in a ''political cover-up''.

Ms Thompson, first interviewed by SBS's Dateline program, accused the Immigration Department of deceiving the detainees and said the system - which she branded ''a farce'' - was designed to force them to give up and return to their home countries. ''We were taking them through a process that goes nowhere,'' she said. ''There is no visa for them to get. There's no legislation governing their resettlement.

''Manus Island is an experiment in the ultimate logic of deterrence, designed to frustrate the hell out of people and terrify them so that they go home.

''Your two options are indefinitely detention or to return to the country where you fear persecution,'' she said.

Ms Thompson said asylum seekers had demanded answers from a senior PNG immigration official at a tense meeting on the Sunday afternoon before the Monday night violence. He had been ''honest with the guys about the fact that there is no process on PNG for their resettlement''.

Her claim is consistent with the account on the Sunday meeting given to Fairfax Media by whistleblower interpreter Azita Bokan and another employee at the centre who has asked that his name not be used.

Mr Morrison last week said he had been ''advised'' that claims the asylum seekers would not be settled in PNG were ''false''.

He said they had been told ''a third country option will not be offered and that neither the PNG nor Australian governments will be acting on behalf of the transferees in seeking alternative settlement countries to PNG''.

But insiders say there is no prospect of resettlement in PNG in the medium term because PNG still has no legal framework to accommodate them, with no guarantees on work and other rights and no progress toward a pilot resettlement scheme.

Meanwhile, Mr Bowles told the hearing in Canberra on Tuesday that Mr Barati's body had been flown to the Papua New Guinea capital of Port Moresby but indicated it had not yet been examined.

''As of today, my understanding is still that the deceased has been moved to Port Moresby in anticipation of an autopsy,'' he said.

Senator Conroy's accusation of a cover-up in relation to last week's Manus Island fatal violence caused General Campbell to say he took ''extreme offence'' at the remark. ''It kind of sounds like a movie, Senator,'' General Campbell said.

''It is a movie, and we're living it Colonel Jessup,'' Senator Conroy said. ''I mean seriously, you can't tell us the truth. You can't tell the Australian public the truth because you might upset an international neighbour.''

Hearing deputy Michaela Cash left in protest, and the estimates committee was suspended by its chairman, Ian Macdonald. Senator Conroy was forced to withdraw the remark and apologise.