Former ACT and Commonwealth ombudsman Allan Asher has launched a stinging attack on Australia's border protection policies, likening immigration detention facilities to Guantanamo Bay.

Mr Asher told The Canberra Times yesterday he had warned the Government, ''week after week'', to find urgent alternatives to keeping people indefinitely detained.

''There's no plan, there's no answer, it's an example where this minister and the Government are avoiding both their ethical and moral responsibilities to vulnerable people,'' Mr Asher said.

''We can't just continue to build up, as Australia is, a de facto Guantanamo Bay and that's what we're doing.''

Mr Asher resigned as ACT and Commonwealth ombudsman last month after it emerged he had scripted questions for Greens Senator Sarah Hanson-Young to ask him at a committee hearing.

As Commonwealth ombudsman, Mr Asher also had responsibility for immigration matters.

His final report to Immigration Minister Chris Bowen, on people kept in detention for more than two years, was tabled yesterday.

It urgently recommended the Government find an alternative to indefinitely detaining people who have been denied security clearance, despite being accepted as genuine refugees.

Asylum-seekers given negative security assessments from intelligence authorities are not eligible for release into community detention.

If they refuse to return to their home countries, or a third country cannot be found, they risk being indefinitely detained in Australia.

Negative ASIO security assessments cannot be appealed and can only be reviewed by ASIO or the Immigration Minister.

''The Ombudsman notes an increase in the number of people detained in an [immigration detention centre] for two years or more who have been found to be owed protection but who have received a negative security assessment,'' Mr Asher's final report, signed on October 7 but tabled yesterday, stated.

''It appears likely that the number of people in this category will continue to grow ... unless the Minister intervenes to grant a visa or approve community detention, these people will remain in a restrictive immigration detention centre indefinitely.''

ASIO director-general David Irvine told a parliamentary committee on Tuesday that any move to give people the automatic right to appeal could raise questions about national security.

He said, ''our assessment tends to come towards the very end of the [assessment] process''.

Mr Bowen's spokesman said the Government made no apologies for its careful stance on security assessments.

''People who have been found to be refugees but have also received adverse security assessments, by law, cannot be granted permanent visas to remain in Australia,'' the spokesman said.

''The Government cannot and will not compromise on matters of national security.''

But Mr Asher said the fact that two-thirds of the Department of Immigration's assessments that people were not genuine refugees were overturned on appeal raised serious questions about the integrity of security assessments.

''It stands to reason that in this security area, these [appealable assessments] would be the same,'' he said.

This reporter is on Twitter: @_biancah