Liberal MPs Trent Zimmerman, Fiona Martin, Dave Sharma, Bridget Archer and Katie Allen crossed the floor to support a crossbench and Labor amendment to protect gay and transgender students from being expelled from religious schools.

The contentious bill passed the lower house following a marathon debate in the early hours of Thursday morning, but the government decided not to proceed with debate in the Senate due to a lack of support.

Dutton claimed the MPs who crossed the floor had blindsided the government about their intention to support the legislation.

“(Scott Morrison) was, frankly, misled … but there are undertakings that were given, the undertaking wasn’t honoured,” Mr Dutton told ABC Radio on Friday.

“The government doesn’t go into a vote like that unless assurances have been given.”

The religious discrimination laws were a major election commitment by Prime Minister Scott Morrison.

It is now unlikely the laws will be debated in the upper house before the next election, due to be held by May, with just two sitting days left for the Senate.

Moderate Liberal senator Andrew Bragg had indicated he was also likely to cross the floor on the issue if debate moved to the upper house.

Finance Minister and government leader in the Senate Simon Birmingham said the issues within the religious discrimination laws were complex.

“These are challenging debates in terms of how you ensure that interplay between those anti-discrimination laws work in a way that respects everybody and protects everybody to the maximum extent possible,” he told Sky News.

“The prime minister has worked through very carefully to ensure that we brought a religious discrimination bill to the parliament, his commitment to that was very clear.”

Senator Birmingham said Attorney-General Michaelia Cash was working through the details surrounding the bill, after it was scrapped from debate in the Senate.

The government was unlikely to have the numbers to pass the bill in the Senate in the form it originally intended, having held urgent meetings with stakeholders after the vote in the House of Representatives.

Dutton said the religious discrimination bill was put to a vote in the lower house due to guarantees being given from Liberal MPs they would support the bill.

“We had very clear statements from a number of people, including beyond the five (who crossed the floor),” he said.

“The prime minister based his judgement, his actions, his decisions on a perfectly reasonable basis following discussions, and it’s difficult when you get to the floor of the parliament and those undertakings aren’t honoured.”

However, Dutton said due to the tight numbers in parliament, the result would have been the same regardless of how many MPs crossed the floor.

The government currently holds 76 seats in the lower house, the bare minimum for a majority in the House of Representatives.