Mr Barilaro agreed his Nationals colleagues would stay in the Coalition at a crisis meeting with Premier Gladys Berejiklian on Friday morning.
The meeting was held after Ms Berejiklian issued an ultimatum to the deputy premier and his Nationals colleagues on Thursday to declare support for her government and to back down on their threats by 9 am on Friday or they would be sacked from cabinet.
Mr Barilaro backed down on Friday morning after blindsiding Ms Berejiklian on Thursday when he announced his MPs would abstain from voting on Coalition bills as they fought changes to the protection plan.
The Nationals are concerned the policy limits land use on farms and the ability to rezone areas for development as more trees are classed as koala habitat, which will restrict the clearing of land.
The move would have effectively robbed the government of its majority and provoked a stern response from the premier.
“It is not possible to be the deputy premier or a minister of the Crown and sit on the crossbench,” Ms Berejiklian fired off in a media statement.
“If required, I will attend Government House tomorrow and swear in a new ministry.”
Mr Barilaro appeared earlier on Friday morning to soften his stance, telling Sydney's 2GB radio he thought the issue could be resolved but it may take time, possibly several weeks.
He also claimed the threat to sit on the crossbench had been misinterpreted.
Bridget McKenzie, the leader of the Nationals in the Senate, strongly defended Mr Barilaro.
“I don't think it's surprising that city-centric policy decisions being made in the main by the Liberal and the Labor Party are being challenged by the Nationals, whether it's in Macquarie St, in Canberra or in Spring St.”
Former Nationals leader Barnaby Joyce also backed Mr Barilaro's tactics, saying the Liberal Party had failed to treat its junior Coalition partner with respect.