It is the second time in less than two years that the Young Nats have parted with the Barnaby Joyce-led National Party on a key policy issue, having resolved in 2015 to support same-sex marriage.

At the time, the aspiring Nationals expressed "disappointment and disillusionment" with their federal leadership.

Mr Joyce has been against any form of carbon trading since coining the phrase "great big new tax" to describe Kevin Rudd's emissions trading scheme - a line later used with lethal effect by then opposition leader Tony Abbott.

The motion to support the introduction of an emissions trading scheme comes three months after the Coalition put an emissions intensity scheme for energy generators on the discussion table before quickly abandoning the idea.

Maintaining the current Direct Action policy, rather than moving to any form of carbon trading, was one of the cornerstones of the Coalition agreement struck between former National Party leader Warren Truss and Prime Minister Malcolm Turnbull after Mr Abbott was toppled in September 2015.

The inter-party agreement also preserves Mr Abbott's compromise position that a plebiscite be held before any move to hold a vote on same-sex marriage in Parliament.

The Young Nationals' stance on carbon trading was described by policy officer Alex Fitzpatrick as one driven by the priority of affordable energy.

"If we do not plan for renewable energy investment, our hospitals and intensive care units, small businesses with cool rooms and the vulnerable will be impacted - whether it's blackouts like in South Australia or higher energy bills," she said.

Ben Franklin, a National Party member of the NSW upper-house, praised the Young Nats for again taking a different position to the wider party, pointing out that it was the youth wing that first backed legal and accessible abortion in NSW in the 1960s.

"I was proud that they debated and passed the motion, that's exactly what Young Nats should be doing," he said.

Mr Franklin, a former long-time state director of the Nationals, was in January appointed parliamentary secretary for renewable energy but he said he was not arguing publicly for an EIS.

But the Coalition government in NSW has done so, telling the Turnbull Government's energy security review headed by chief scientist Alan Finkel that he should "consider the need for a mechanism that provides market signals" for the transition to a more diversified and renewable energy mix.

The motion taken by the Young Nats brings them into line with the National Farmers' Federation, the Business Council of Australia, the Australian Industry Group and much of the energy sector, including the electricity transmission and distribution businesses.

Comment has been sought from Mr Joyce.

Labor's spokesman for energy and climate change, Mark Butler, welcomed the schism in the Nationals.

"It's good to see the future of the National Party understands the importance of energy security and affordability," he said.

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