Security agencies will gain greater access to encrypted messages after a Labor backdown allowed the Federal Government to pass its legislation on Parliament's final sitting day.

Key points: Labor pulls its amendments to encrypted message access bill and votes to support the Government

Labor pulls its amendments to encrypted message access bill and votes to support the Government Bill Shorten claims he has a deal that the laws will be improved when Parliament returns in February

Bill Shorten claims he has a deal that the laws will be improved when Parliament returns in February The Government has pledged to only support amendments consistent with a parliamentary report

Labor had planned to amend the legislation, which it has repeatedly described as flawed.

But late on Thursday Opposition Leader Bill Shorten announced Labor would pass the laws provided the Coalition agreed to make certain changes in the new year.

Labor then pulled its amendments in the Senate and the bill was passed before Prime Minister Scott Morrison had even responded to Mr Shorten's request.

Attorney-General Christian Porter later announced the Government had agreed to "consider" Labor's amendments "if any genuinely reflect the recommendations of the Parliamentary Joint Committee on Intelligence and Security".

The arrangement ended a day-long stand-off between the Government and Labor.

The bill was passed before Scott Morrison had even responded to Bill Shorten's request. ( ABC News: Ian Cutmore )

Labor and the crossbench had the numbers in the House of Representatives to force a vote that would have meant more refugees coming to Australia from Nauru and Manus Island.

However, delays in the Senate dealing with that meant the Upper House was not able to change the encryption bill if it wanted it to become law this year.

"Do I go home and say 'well I hope nothing happens and I hope that the Government's politics don't backfire on the safety of Australians'? I'm not prepared to do it," Mr Shorten said.

Labor's backdown came two hours after Mr Porter accused Labor of putting national security at risk.

"It became a pawn and a hostage to a larger game trying to embarrass the Government, and it's very, very unfortunate for the Australian people," Mr Porter said.

"Ultimately Bill Shorten and Labor put a tactical political ploy ahead of legislation that would have enhanced Australian safety."

Sorry, this video has expired Attorney-General accuses Labor of risking Australian's safety over encryption bill changes

Concerns about the new laws linger

The Law Council of Australia slammed the major parties for creating a law that both sides of politics concede needs changes.

"The half-amended encryption access laws rammed through the Senate are better than the original, but serious concerns remain," Law Council president Morry Bailes said.

"We now have a situation where unprecedented powers to access encrypted communications are now law, even though the Parliament knows serious problems exist."

Vanessa Teague, an expert in cryptography at the University of Melbourne, said the debate over what constituted a "systemic weakness" had been central to criticisms of the bill.

The laws mean police can request technology companies to build in features that would give access to encrypted communications.

But companies will not have to introduce such features if they are considered "systemic weaknesses" — that is, they are likely to result in weakened security for others.

Earlier drafts of the bill failed to define the term at all, but even the definition introduced at the last minute is contested.

Dr Teague said the new laws also failed to address the concerns of technical experts.

"The whole question all along has been, whether by targeting an individual user, they are accidently jeopardising everybody else's security," she said.