The Australian newspaper reported on Wednesday the former prime minister had let the government know he would not vote for the target if it came to parliament.
Mr Abbott went further, also writing an article for The Australian arguing it would be "unconscionable for a government that was elected promising to scrap the carbon tax and to end Labor's climate change obsessions to go down this path".
Mr Joyce said backbenchers were at liberty to do what they like but there was a fundamental responsibility to ensure stable government.
"I don't think a former prime minister is going to move to put a Labor government into power," the deputy prime minister told Sky News on Wednesday.
"No matter what statements have been made, they know full well the best sort of government you have is one where people who actually understand business are operating the show."
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He said all coalition MPs should wait to see the government's final position on a long-term energy policy.
Assistant minister, Liberal senator Anne Ruston, said a "suite of measures" were on the table and differences of opinion could be managed.
Senator Ruston said Mr Abbott was entitled to his view but she hoped he could be persuaded by a strong argument.
"I happen to disagree about the way he's going about things but we just need to go through a process and I am sure the party room as it always does will come up with a decision that's in the best interests of the Australian public for affordable and reliable power," she told ABC radio.
Labor frontbencher Amanda Rishworth said Mr Abbott's aim was to cause as much "chaos and trouble" as possible.
"The test is really for Malcolm Turnbull ... will he stand up to these conservatives on his backbench and deliver what (Chief Scientist) Alan Finkel said is critical to the long-term reliability and affordability of energy and
that is a clean energy target, or is he going to capitulate to a noisy few on the backbench?" Ms Rishworth said.
Mr Abbott, who lost the Liberal leadership to Mr Turnbull in September 2015, is also facing pressure from grassroots members of the party.
A Victorian branch of the party passed a resolution in August expressing concerns about his destabilisation and called on the federal party to explore options to disendorse him as the candidate at the next election.
Former Northern Territory chief minister Paul Everingham was quoted earlier this year as saying he would be happy to endorse a motion to expel Mr Abbott or at least have him disendorsed for "disloyalty".
