Legislation cracking down on hate speech will create new offences for threatening force of violence against particular groups, including on the basis of race, religion, sexual orientation, gender identity, disability or political opinion.
But the opposition pushed to add mandatory minimum prison sentences for the display of Nazi and terrorist symbols, and some terrorism offences.
The display of Nazi or terrorist symbols will carry a one-year mandatory prison sentence, three years for financing terrorism and six years for other terrorism offences under amendments put forward by Home Affairs Minister Tony Burke.
This can be mitigated by up to 25 per cent if there is co-operation with law enforcement.
The amended legislation passed the lower house on Thursday. It will need to pass the Senate before it can become law, but is all but confirmed to be waved through with the support of the coalition and Labor and a vote forced for Thursday.
It comes following a rise in anti-Semitic attacks, particularly in Sydney and Melbourne, including the arson of a synagogue and a caravan filled with explosives being found with a list of Jewish targets.
Two men were charged in Western Australia on Wednesday following a spate of anti-Semitic graffiti in Perth over the weekend.
Prime Minister Anthony Albanese was critical of mandatory minimums after the coalition announced its plan to pursue them before backflipping on Wednesday.
Labor's policy platform is also opposed to mandatory minimums, arguing they don't work and take away judicial independence.
The Greens and several independents voted against the amendment.
Labor also passed a coalition amendment to add advocating force or violence by causing damage to property to the legislation.
Opposition home affairs spokesman James Paterson welcomed the minimum prison time, saying it would "reassert deterrence to send a strong signal to the people responsible for this campaign of terror".
Added benefits included perpetrators being behind bars for longer and victims getting a stronger sense of justice, he said.
"The prime minister and his senior ministers rubbished the need for any mandatory minimum sentences but they have now conceded under political pressure that they are necessary," he told reporters in Canberra.
Mr Albanese wouldn't comment when asked why he rolled over for the coalition's demand to mandatory minimums despite Labor's opposition.Â
"I want people to be held to account, people who are committing crimes to be held to account for them," he told ABC TV on Thursday.
"Putting this in place and then having a review of how the laws are operating by the Joint Parliamentary Committee on Intelligence is an appropriate thing to do and something that we've worked through."
"I want the entire parliament to work together to make sure that we stamp out anti-Semitism."
Normal caucus procedures were followed, Mr Albanese said, although partyroom was kept in the dark about the government's amendments at the start of the week.
Amendments or legislation can sometimes be tabled before being brought before caucus to tick off but is then retrospectively presented at the next meeting.
It is understood cabinet didn't meet on Wednesday either ahead of the amendments being tabled late in the evening but it did meet on Monday.
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