Federal Labor has accused the Coalition of bungling native title changes and breaching a deal struck between the major parties.

The Coalition moved to amend the Native Title Act in February soon after a court scuttled a multi-million-dollar deal between the West Australian Government and traditional owners.

The Federal Court rejected the Indigenous Land Use Agreement (ILUA) between the parties because it was not signed by all native title claimants.

Until February's court decision, ILUAs could be made without the support of all native title applicants.

The court ruling overturned years of established law, throwing doubt over current and future agreements nationwide.

The Coalition and Labor agreed on the need to amend the legislation to reverse the effect of the recent court decision, allowing at least 126 ILUAs already proposed or registered to continue with as few as one claimant.

But the Opposition claims Attorney-General George Brandis has proposed changes that go beyond what the major parties agreed during a Senate committee process.

Shorten 'uncomfortable' with Government handling of issue

In a letter to Prime Minister Malcolm Turnbull on Friday, Opposition Leader Bill Shorten accused the Government of "repeated breaches of faith".

"These amendments failed to deliver on the prior agreement and were again defective in a number of respects," the letter said.

"It is once again clear that these new amendments have not been subjected to any form of consultation with legal experts, Indigenous Australians or industry.

"The repeated breaches of faith by your Attorney-General in this matter, and the clear unwillingness of your Government to properly consult on the significant issues at hand, have meant that Labor remains concerned about some aspects of the bill."

The correspondence was also signed by shadow attorney-general Mark Dreyfus and shadow assistant minister for Indigenous affairs Pat Dodson.

The letter said Labor wanted the Senate committee's recommendations enacted "as quickly as possible" and offered to work with the Coalition over coming weeks.

A spokeswoman for the Attorney-General's office slammed Labor for "playing politics" with Indigenous affairs.

"The Government's primary objective is to restore the status quo following the McGlade decision [in February]," she said.

"The Government, at all times, worked constructively with Labor and native title stakeholders so that the bill could be passed by the Parliament before the Easter break.

"Labor's latest political stunt however means Aboriginal people will be left waiting until at least May.

"The Government remains committed to these reforms and calls on the Labor Party to put certainty for stakeholders ahead of politics."

The amendments have not been debated in the Senate.

Parliament next sits in May.