NSW Deputy Premier and Nationals Leader John Barilaro to take mental health leave, deputy Paul Toole will take over the position in his absence.

Mr Barilaro informed his Nationals collegues via text message.

In a statement, NSW Premier Gladys Berejiklian said Mr Barilaro on Friday afternoon advised her he would be taking four weeks of personal leave.

"I have offered him any support he may need," Ms Berejiklian said.

"I wish John and his family all the best during this time."

Mr Barilaro's decision means he will miss a crucial debate on the Government's koala protection policy when the Cabinet meets on October 6.

His time off comes after political turmoil for the NSW Coalition which erupted last week when Mr Barilaro threatened to take his Nationals team to the crossbench.

Ms Berejiklian called their bluff, and said they had to resign from their ministerial positions if they were to sit on the crossbench.

The stoush was over the Government's koala protection policy, which Mr Barilaro described as a "nail in the coffin for farmers".

Under the policy landowners will be required to jump through more hoops to ensure koalas were not at risk if the land were to be cleared for development.

There have been six months of closed-door negotiations between Mr Barilaro, Ms Berejiklian and Planning Minister Rob Stokes over the policy.

But it wasn't until earlier this month that the Nationals expressed their dissent.

Barilaro 'doing his best'

National Party senator Matt Canavan told Sky News he wished Mr Barilaro "all the best" during his leave period.

"He's a good mate of mine, yes, he has had a fairly tumultuous couple of weeks," Senator Canavan said.

He said Mr Barilaro had been "doing his best" to fight "pretty mad planning laws in NSW that take away people's property rights".

"That has put him under intense scrutiny and this can be a pretty tough environment at times, so I wish him and his family all the best the next few weeks and I do hope we get good results for farmers and property owners of NSW."

Mr Canavan defended Mr Barilaro's approach to the disagreement with his Coalition partners.

"The process sometimes with the National Party is not pretty but we have to be effective — and it may not be pretty but sometimes it's pretty effective," he said.

"It's pretty effective to bang the drum sometimes and get results. We have to do that from time to time because frustratingly you don't get heard otherwise."