The Nationals delegates voted to oppose a clean energy target – a policy that was recommended by Chief Scientist Alan Finkel in his recent report on the energy market.
Mr Joyce left the room before the vote was held, but on Monday morning told ABC Radio the Nationals were “guided” but not “instructed” by the views of members.
The internal vote exposes the differences of opinion within the Coalition over energy policy.
The Turnbull government has adopted 49 of Finkel's 50 recommendations, but the clean energy target remains a controversial sticking point.
Mr Joyce said energy policy was formulated together with the Liberals.
“Everything in the Coalition's a compromise,” he said. “It's a business arrangement, it always has been.”
He said the strong anti-renewables vote was a reaction to rising power prices in rural areas. But he conceded that Australia would need to use subsidies to encourage the use of renewables like solar and wind to meet its obligations under the Paris climate agreement.
“I believe that we've got to comply with our international agreements... if you negotiate them you've got to comply with them,” Mr Joyce said.
“They're essential subsidies if you want to comply with your international agreement.”
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The internal Nationals push against the clean energy target comes as the head of energy retailer AGL, Andy Vesey, heads to Canberra for meeting with the prime minister.
Mr Vesey will sit down with Malcolm Turnbull and the energy minister Josh Frydenberg to discuss the future of the Liddell coal-fired power station, slated to shut down in 2022.
The government wants the life of the plant extended by five years to help patch predicted shortfalls in power supply.
But AGL has committed to abandoning coal, raising the prospect of a last-minute sale rather than a closure.
Mr Frydenberg said he was looking forward to a “constructive conversation”.
“We need to ensure as far as possible that there is no shortfall,” he told waiting media at Canberra Airport on Monday.
Mr Joyce said the Nationals were committed to coal as a “medium-term” power solution.
“Keep the coal-fired power operating, so the lifts work, and the traffic lights work, and the hospitals can continue to do operations until the end of January – rather than shut the whole show down,” he said.
