A decision to introduce federal mandatory sentencing laws has been slammed by Senator Lidia Thorpe as going against the "best evidence" on effective justice systems.

The legislation, which has been supported by the Coalition, was also been criticised by an elder Labor statesman Kim Carr, labelling it "profoundly disappointing".

The Labor government's hate crimes legislation, which has come amidst an increase in antisemitism and islamophobia across the country, passed the lower house on Thursday morning after an amendment was implemented to introduce mandatory sentences.

"We are sending a clear and unambiguous message that advocating or threatening violence is not acceptable. It is criminal behaviour and will be treated as such," Attorney-General Mark Dreyfus said in a statement on Thursday afternoon.

Mandatory sentences include six years for terror offences, as well as three years for financing terrorism and one year for displaying hate symbols.

Senator Thorpe said whilst it was "critical" Australia tackles "racism and hate," she couldn't support legislation that imposed mandatory sentencing.

"This bill could have been an opportunity to take a step in the right direction. But instead of working with the crossbench, Labor has teamed up with the Coalition to ram through unjust legislation that goes against best evidence," she said.

The assistant minister for Indigenous health, Ged Kearney, abstained from voting on the amendment to the bill, which was supported by both major parties and independents Allegra Spender, Rebekha Sharkie, Dai Le, and Russell Broadbent.

It was opposed by the Greens and other cross-benchers.

"Mandatory minimum sentences don't reduce crime, they undermine the independence and discretion of the judiciary, and lead to unjust, discriminatory outcomes. This is what the Labor party platform itself says," Senator Thorpe said.

Labor's national platform says the practice of mandatory sentencing "does not reduce crime but does undermine the independence of the judiciary, lead to unjust outcomes and is often discriminatory in practice".

The decision, which was made public late on Wednesday night, is a dramatic shift by the government after they initially resisted calls by the Coalition for mandatory jail terms after a package of measures to combat antisemitism was announced last month.

Prime Minister Anthony Albanese initially said offering mandatory sentences was "fraught" and "counterproductive," before changing his tune on Thursday, arguing, "I want people to be held to account".

A former long-time Labor Senator, Mr Carr told Guardian Australia it was a "clear breach" of the platform, only enacted as a short-term fix to a political issue.

"There is no doubt there's a short-term political assessment, hopefully to get this issue off the table, which you will not achieve," Mr Carr said.

"It usually reflects that the government is under considerable pressure, and for short-term relief will find that a long-term precedent is set."

Speaking less that 24 hours before the change of tact by the government, Labor MP Labor Mike Freelander, who is Jewish, told the house he didn't believe in mandatory sentencing, arguing "we should trust in the legal process".

"We do have the separation of powers and we do need to trust in the legal process to make sure that people are appropriately punished for the crimes they commit – and these are crimes. They're terrible crimes," he said on Tuesday.

Independent MP Andrew Wilkie was highly critical of the amendments, arguing it was up to the "courts to decide punishment, not politicians".

"For the major parties to push through mandatory minimum sentencing on the Hate Crimes Bill today shows once again their contempt for due process and matters of principle," he said.

Fellow independent MP, Kate Cheney, agreed, arguing Kate Chaney, "hate crimes need serious consequences but courts should decide sentences, based on all the circumstances".

Senator Thorpe, who has been open in her support around Palestinian causes since Israel's assault on Gaza in the aftermath of October 7, said by listening to opposition leader Peter Dutton, it was another "shameful instance of Labor betraying their member base and lurching to the right".

"These parties pretend to be on opposite sides, but when it comes to expanding surveillance and criminalization, including of kids as young as 10, they are in lockstep," the Gunditjmara and Djab Wurring Senator said.

"Antisemitism is a form of racism. The anti-discrimination laws and the Race Discrimination Act are not fit for purpose and require urgent review. We must join every other democracy in the world and legislate an enforceable National Human Rights Act."