The Federal Government says the 157 asylum seekers at the centre of a High Court fight could have posed a security threat if they were told where they were going.

The 157 Tamil asylum seekers were held on a Customs ship for almost a month before being transferred to the Curtin Detention Centre in Western Australia.

Court documents have revealed the Government came very close to offloading the group in India, but was halted by an urgent interim injunction last month.

According to the Government's defence, filed on Thursday, the Customs ship carrying the group arrived near India and was resupplied while the High Court case played out.

In the week Immigration Minister Scott Morrison was holding talks with the Indian government, the plan was abandoned and the Tamils were transported to Australia's Cocos Islands.

While secrecy prevails around Operation Sovereign Borders, the documents reveal concerns the Tamils would be a security threat if they were given information about their destination.

"If the passengers from the Indian vessel were informed significantly prior to their arrival that they were being taken to India, they would take steps to prevent their effort to reach Australia from being thwarted," the defence case states.

Counsel for the Government, Stephen Donaghue, argues the Tamils would have threatened or engaged in self-harm and would have jeopardised the safety of the crew.

There were 35 maritime officers and 21 crew on board.

The court documents make no mention of the orange boats used to send asylum seekers back to Indonesia. Earlier this week, Mr Morrison refused to be drawn on operational details.

Under an agreement with India, the 157 asylum seekers will be assessed by Indian consular officials at Curtin and could be sent back to that country.

However, the asylum seekers must first agree to speak to the officials.

The Immigration Minister has said the Tamils would be processed offshore if they did not cooperate with the Indians.

The Ocean Protector's role in future missions is in doubt with the Government's lease on the ship not being renewed at the end of the year.