Western Australia wants a clean slate for its legal battle with Clive Palmer after the federal government withdrew its support for his borders challenge.

The matter will return to the Federal Court on Friday for a case management hearing sought by the WA government, which will argue the case should be vacated and a new trial of the issues convened.

It comes after Prime Minister Scott Morrison wrote to WA Premier Mark McGowan saying the Commonwealth would no longer support the challenge after taking into account the evolving state of the pandemic in recent months.

WA Attorney-General John Quigley says the situation has “shifted dramatically” and the evidence tendered by the Commonwealth should be struck out.

“What we are urging is that the Commonwealth, in view of its changed position, support Western Australia in saying there should be a new hearing where it’s all clean,” Mr Quigley told 6PR radio on Thursday.

The prime minister on Thursday signalled he would support the request, saying there was no quarrel between he and Mr McGowan.

“I believe our response will assist what they’re seeking to do,” Mr Morrison told reporters in Canberra.

Mr Palmer, who was denied an exemption to WA’s hard border closures, is challenging the restrictions on the basis they are unconstitutional.

A ruling had been expected in the High Court in October after a four-day hearing wrapped up in the Federal Court last week.

That ruling is almost certain to be delayed if a new trial of issues is ordered.

Federal Attorney-General Christian Porter this week said the Morrison government had decided its intervention in the matter was degrading its ability to work cooperatively with WA.

Mr Porter was one of several federal WA MPs who risked a potential electoral backlash from the Commonwealth’s intervention in the Palmer case given the overwhelming support for border closures among West Australians.

WA’s Labor government had already begun campaigning against the intervention of the “Liberal Party” in the matter.

The legal battle has fuelled animosity between Mr McGowan and Mr Palmer, who the WA premier has labelled “Australia’s greatest egomaniac”.

Mr McGowan has linked the billionaire’s entry bid to his purchase of almost 33 million doses of hydroxychloroquine, an anti-malarial drug touted by US President Donald Trump which has since been found to be ineffective at treating COVID-19.