Two men were taken into custody in Melbourne and Sydney while a woman was detained in Perth.

None are allowed to know the reasons the Australian Security and Intelligence Organisation has labelled them a threat to national security nor to appeal the assessment.

The latest cases come as the High Court prepares to hear a challenge to the ASIO assessment regime on June 18, brought by the same legal team that scuttled the government’s planned people-swap deal with Malaysia.

The legal challenge is compounding Labor’s difficulties in the politics swirling around border protection after reports this week that a people smuggler fooled immigration authorities by claiming refugee status and set up criminal operations in Australia.

Yesterday, Immigration Minister Chris Bowen’s office confirmed that the man, known as ‘‘Captain Emad’’, still holds a valid Australian visa, despite fleeing the country on Tuesday night 24 hours after ABC’s Four Corners alleged he was a people smuggling kingpin.

The opposition fuelled the political storm, saying Mr Bowen should have known about a two-year federal police investigation into Captain Emad before the allegations were aired on television.

Police said they could not prevent Captain Emad departing Australia as there was insufficient evidence to lay charges.

The government is refusing to say when, or if, it was told police suspected Captain Emad had lied about being a refugee and was fraudulently living in Canberra in taxpayer-funded housing.

The three blacklist refugees join 51 others now held in indefinite detention - recognised to be too much at risk to return home but not permitted a visa for release into Australia.

The woman, believed to be in her early 30s, fainted after being told on Thursday that ASIO had put her on a blacklist and had to be taken to hospital.

She had been living in Perth since late last year after being released from detention, but is expected to be eventually transferred to a Sydney detention centre.

The government has been rebuffed by the United States and Britain in attempts to send some of the refugees to join family overseas.

Adverse assessments are given to fewer than 1 per cent of all asylum cases but the issue is a growing headache for Labor, with the surge in people seeking refugee status in recent years increasing the number of people trapped in what one MP has dubbed a ‘‘legal blackhole’’.

Backbenchers are agitating for a review mechanism for the ASIO findings, in line with a pledge made at the ALP national conference in December. But the government has so far failed to change the rules.