Scott Morrison ignored his department’s advice that it was illegal for him to refuse permanent visas for boat arrivals found to be refugees, and defied warnings from bureaucrats that the move would be challenged in the high court and he would lose.

The minister for immigration personally ordered protection visa numbers be capped for 2014 – to avoid granting permanent protection to any boat arrivals – before his action was ruled unlawful by the full bench of the high court.

Overruled by the judiciary, Morrison has since employed a previously unused “national interest” clause in the Migration Act to issue unchallengeable “conclusive certificates” to refuse visas, but this is also being contested in court.

Lawyers for the minister are back in court in December.

Documents before the high court show Morrison was told on 15 January, in a brief from his department, that his policy objective of never granting permanent protection to boat arrivals could not be achieved “in the medium to long term” but that he could “delay being forced to grant” visas in the short term.

The departmental brief is confidential, but sections of it are reproduced in submissions before the high court.

The brief gave Morrison five strategies “to delay being forced to grant a permanent protection visa in the absence of a new temporary visa”, but conceded “each of these strategies is likely to be short lived as a consequence of decisions taken in parliament to overturn them or in the courts to invalidate them”.

The first strategy was to reintroduce temporary protection visas by regulation. This was done but then disallowed by the Senate.

Another of the strategies proposed, and ultimately undertaken by Morrison, was to unilaterally cap the number of permanent protection visas so that no more could be granted to boat arrivals.

In June the full bench of the high court unanimously ruled that Morrison “did not have the power … to limit the number of protection visas that may be granted”.

The department brief had warned him six months earlier it was illegal, and a court challenge could be “expected to be lodged almost immediately”.

But the move would buy Morrison some time, the brief said.

“Any decision by the high court that use of the cap was invalid would then be some months away,” it said.

The brief even included a flow-chart which indicated how long the obligation to grant visas could be delayed by each strategy.

In one synopsis, the department hoped the high court would defy expectations and rule Morrison’s actions were legal: “Possible temporary protection visa disallowance responses; best case scenario – high court may do the unexpected.”

The high court case in December concerns a Pakistani boat arrival who has been in immigration detention on Christmas Island since May 2012.

He is an ethnic Hazara and a Shia Muslim. Australia has found he is a refugee, with a well-founded fear of persecution by Sunni extremists in his home country.

He has passed all security and character checks.

It is illegal for Australia to send the man back to Pakistan. Immigration authorities are obliged to grant him a visa, the high court said.

The man was initially allowed to apply for a visa, but legislative changes and Morrison’s imposed cap on visa numbers have stalled the process.

After the high court ruled the government was “bound to … grant him a protection visa”, Morrison issued a “conclusive certificate” – which cannot be appealed – ruling it was not in the “national interest” for him to have a visa.

The man remains in immigration detention.

“The issue at the heart of this proceeding is whether the minister may achieve by administrative fiat the outcome presently denied to the minister through the parliament,” Stephen Lloyd, acting for the Pakistani man, told the high court.

“The minister seeks to use mechanisms under the Migration Act to attain an unlawful end.”

Stephen Donaghue, for the government, told the high court Morrison did have the power to limit the number of visas to be granted, and that the government must keep “unlawful non-citizens” in detention while a visa determination was made.

Donaghue told the court there was “no duty” on Morrison to grant a visa to a person found to be a refugee and requiring Australia’s protection. Morrison was able to insist upon additional criteria to be met before granting a visa, he said.

Morrison’s office has not yet responded to queries from Guardian Australia.