Labor, the Greens and crossbenchers teamed up in a vote late on Tuesday to torpedo new regulations allowing ARENA to invest in the federal government's favoured "low emissions" technologies, including carbon capture and storage and "clean hydrogen".

The rare defeat in parliament came less than a week after a Liberal-chaired committee and the independent Parliamentary Library cast doubt over the legality of the new regulations, on the grounds the agency was established with singular purpose of backing renewables.

The Parliamentary Library's advice suggested the changes could be invalid and vulnerable to legal challenge, which would would place "considerable uncertainty" over projects supported under the new regime.

Department officials had previously insisted the changes were "quite legitimate" and believed they would survive legal challenge.

Labor and the Greens' attempt last week to block the ARENA overhaul was voted down in the House of Representatives, where the Coalition holds an absolute majority.

But the two parties were successful in the Senate, securing a one-vote victory with the help of independents Jacqui Lambie and Rex Patrick.

The government will be rueing the absence of One Nation senator Pauline Hanson, whose vote on Tuesday night would have tipped the Coalition over the line.

Energy Minister Angus Taylor slammed Labor after the vote, saying its decision to team up with the Greens would result in the loss of $192 million in planned investment and 1400 jobs.

"Labor has walked away from clean tech jobs, and blue-collar jobs," he said.

"Despite the Australian Labor Party platform explicitly supporting these technologies, every Senator in the Australian Labor Party room has now voted against them.

"It has not only shown that Labor is economically reckless, but that their promises cannot be trusted."

Labor's climate and energy spokesman, Chris Bowen, dismissed Mr Taylor's attack, arguing if that the government wanted to fund technologies such as carbon capture and storage it could so so through other programs.

"This [change] was always wrong, it was probably illegal," he said.

"It is just the latest attack on ARENA and CEFC [Clean Energy Finance Corporation] by a government which is prejudiced against renewable energy.

"Angus Taylor doesn't believe in renewable jobs."

Labor Hunter MP Joel Fitzgibbon criticised his party's stance.

"It will take more than wind turbines and solar panels to create a cleaner economy," he said. "We need a broad mix of technologies including carbon capture and storage, and those which reduce vehicle emissions.

"We should never vote against more money to do more things, regardless of the agency being used to spend the money."

Greens leader Adam Bandt said Tuesday night's vote was a "really big win for climate".

"As a result, the government cannot use public money to fund coal and gas projects through the renewable energy agency," he said.

Our journalists work hard to provide local, up-to-date news to the community. This is how you can continue to access our trusted content: