The Queensland government has made an 11th hour backflip on a secret policy to contest every new native title claim in court, on the eve of being hauled before the federal court to explain themselves.

But the Liberal National party’s position appears to still be unclear after Queensland natural resources minister, Dale Last, doubled down on contesting native title in a statement to Guardian Australia on Tuesday.

Most native title claims are consented to by both parties – typically a traditional owner group claiming the land right and the state government – before being signed off by the federal court in a consent determination hearing. Few claims are litigated in a contested court hearing, which is more expensive, slower and more complex for the applicant.

But in February, the Queensland natural resources minister, Dale Last, ordered that all native title claims should be contested. That instruction was revealed in an affidavit made by the acting director general of the department of natural resources and mines, manufacturing and rural and regional development, Amy Rosanowski, who was issued a please explain by the federal court this month during a hearing into the decade-old native title claim by the Cape York United #1 claim group.

Chief justice of the federal court, Debra Mortimer, said in a court order seen by Guardian Australia that the state had decided to oppose parts of the claim it had previously accepted, “and seeks to have those areas proceed to trial”.

On Friday 6 March, Mortimer ordered Rosanowski to explain by the following Monday why the state had changed its position.

In an affidavit, Rosanowski said that the director general, Graham Fraine, passed on an order from Last on 17 February, “that native title determination applications should be contested”. He later went on leave. Rosanowski passed the instruction on in an all-staff forum two days later, she said.

“I instructed NTILS (Native Title and Indigenous Land Services) officers a) to cease reviewing connection materials for the purpose of reaching consent determinations in this proceeding in relation to this area,” she said.

Rosanowski also ordered public servants to advise the applicant in the Cape York claim that the state “does not accept connection”; and “that the undetermined area should proceed to trial”.

Following the instruction, the department “raised a number of issues concerning the direction,” Rosanowski wrote in her affidavit.

She then said she spoke with the minister on 9 March and “was advised he no longer considered this undetermined area should proceed to trial”.

Rosanowski signed and lodged her affidavit the next day and the matter was heard before the court on Thursday 12 March..

“The minister further informs me he does not require all other undetermined areas to proceed directly to trial,” the affidavit read.

“The state’s current position is that connection in this area is accepted in principle.”

However Last pointed to again contesting native title in his statement to Guardian Australia, saying: “the government believes Queensland should be open and available for all Queenslanders”.

“The government has a responsibility to represent the interests of all Queenslanders and a duty to ensure the way the State participates in native title matters meets this expectation,” he said.

The court on Thursday heard a number of claims have been stalled after the state ceased negotiating following the February policy shift.

Mortimer said the change had “put into a state of uncertainty what is happening in Queensland about native title claims”.

“That’s part of the reason that we’ve – I’ve – called this case management hearing today,” Mortimer said.

She asked the state whether the minister’s direction related only to some claims, or if it applied to others that she said had been sidetracked.

Solicitor general Gim Del Villar, who acted for the state, told the court that “the state does not have a blanket position that it is going to take matters throughout the state to trial”.

“Whether or not the state decides to take a matter to trial will depend on the evidence and particular circumstances of the particular case,” he said.

Del Villar said he didn’t “apprehend” that the state’s position was different after the reversal than it had been before the minister’s order.

Dan O’Gorman, representing the claimant, said his client was “relieved … to learn that apparently, now nothing has changed”.

“Your honour, the applicant believes there’s nothing to be gained by commenting upon the events that took place between the 17th of February and the 10th of March,” he said.