The Senate has rejected the Government's emissions trading scheme a second time, giving Labor a trigger for a double dissolution election.

The Senate has voted 41 to 33 to reject the legislation setting up the carbon pollution reduction scheme.

The vote, taken at 11.47am today, followed more than 40 hours of debate in the upper house.

Liberal senators Sue Boyce and Judith Troeth voted with the Government, but their support was not enough to give Labor a majority.

The crossbench, including the Australian Greens, voted with other coalition senators.

Prime Minister Kevin Rudd had wanted the deal - negotiated with ousted Liberal leader Malcolm Turnbull - passed before the UN climate change summit in Copenhagen, starting on December 7.

New leader Tony Abbott, who was elected on Tuesday, immediately withdrew Opposition support for the bills.

"The Senate has delivered a big win to the people of Australia who have been saved from a massive new tax that would have been foisted on them without proper scrutiny," Mr Abbott told reporters.

Mr Abbott has said it would be "folly" for Australia to establish an emissions trading scheme before the United States had settled on its model and before Copenhagen.

He said the senators who voted against party policy would not be punished.

"I respect what senators Troeth and Boyce did, there'll be no recriminations," Mr Abbott said after the vote.

"I respect their position, they respect the party's position.

"In our party, people have that right, it's good that it's exercised rarely."