In two unanimous decisions, with implications for thousands of boats arrivals, the full court ruled that Immigration Minister Scott Morrison's decision to impose a cap on the number of places in Australia's refugee intake for boat arrivals was invalid.

The government's determination to deny permanent protection visas will now rest with the Senate, where the Palmer United Party will control the balance of power from next month.

The party's leader, Clive Palmer, has spoken out strongly in support of refugees, but told Fairfax Media the party would study the High Court judgment and any decision on allowing temporary protection visas would be made by his party room.

Mr Morrison re-imposed the refugee intake cap in March after the Senate voted down his attempt to re-introduce temporary protection visas (TPVs) for boat arrivals, declaring that the Coalition would "not give an inch when it comes to protecting our borders".

He vowed then to take "every step necessary to ensure that people who arrive illegally by boat are not rewarded with permanent visas". Mr Morrison, who has presided as minister over six months without a boat arrival, was travelling when the judgment was handed down and was unavailable for comment.

His March decision effectively imposed a freeze on the grant of permanent protection visas to about 1400 asylum seekers who had already been found to be refugees and has implications for many thousands more whose claims have not yet been decided.

"This is a very significant victory for the rule of law being brought to bear on the plight of refugees in our country," said lawyer David Manne, who led the legal team representing an Ethiopian teenager who arrived in Australia without a visa last year, after stowing away on a cargo ship.

A second decision upheld a challenge on behalf of a Pakistani national who arrived by boat at Christmas Island in 2012.

In both cases, the court ordered Mr Morrison as minister to consider and determine the asylum seekers' applications for a protection visa according the law as it stands.

Labor and the Greens welcomed the decision, with Labor's immigration spokesman, Richard Marles, saying: "Putting a freeze on the issuing of protection visas just because the Senate rejected the government's TPVs was always an act of petulance which caused great misery."

Greens senator Sarah Hanson-Young described the ruling as "a win for fairness and decency", saying: "The court has ruled that the Abbott government's cruelty for cruelty sake is illegal. This decision will allow refugees to start rebuilding their lives here in Australia."

Sister Brigid Arthur, who acted as "litigation guardian" for the Ethiopian boy, said it was "very good that he will now have some certainty about his future".

Mr Manne, who also led the legal team that successfully challenged the Labor government's "Malaysian solution", said the latest decision had "potentially major implications" for thousands of refugees who arrived by boat.

"The law of Australia is that there is only one protection visa, and that's a permanent protection visa for refugees. What this means is that the government must get on with the grant of a visa which our client is entitled to as a refugee," he said.

He said the life of the boy had been in limbo since Mr Morrison imposed the freeze.

In their written judgment, justices Hayne and Kiefel said they had taken into account the consequences for the detention of those who came unlawfully and the time limits for determining protection visas.

smh.com.au