Ms Ley said she called the former deputy prime minister "to check in" but would not give further details about the conversation, with speculation Mr Joyce will defect to One Nation.
"I did give Barnaby a call because, you know, we've been colleagues in parliament for a long time," she said during a Q&A session at a Centre for Independent Studies event in Sydney.
Mr Joyce announced plans to leave the Nationals and says he won't contest his regional NSW seat at the next election.
The outspoken MP also confirmed he has had two conversations with One Nation leader Pauline Hanson, but insists a formal change in his allegiance is not locked in.
"I think they do a good job," he said about Senator Hanson's hard-right party on Monday.
"On (net zero), I suppose One Nation is not barking mad like others are.
"I'm not saying yes, I'm not saying no. I'm saying I'm not going to entertain this discussion," Mr Joyce told the ABC.
He said his "less than spectacular" relationship with Nationals leader David Littleproud contributed to his plan to leave the junior coalition party and his decision not to recontest his seat of New England at the next election.
Mr Littleproud said his predecessor would not be forced out of the party room, and any decision on Mr Joyce's political future lay squarely with the New England MP.
"The ball's in his court if he wants to be part of the party room," he told Sky News.
"Nothing's changed. It's up to him in terms of where he wants to go next. We've made it very clear he's welcome."
But Mr Joyce said his relationship with the Nationals leader has broken down.
"I don't think it's conducive to a harmonious party room for them or, to be honest, for me," he said.
"I think it is playing silly games of charades that everything is fine and anything is going well - it wasn't."
While the former Nationals leader has been happy to break with the party line in the past, particularly on climate policy, University of New England politics expert Karin von Strokirch said One Nation could be a more natural home for Mr Joyce.
"One Nation would give him free rein to say whatever he likes," she told AAP.
"They're in tune with his views on climate change and net zero and renewable energy.
"That's what he's been in trouble for with the coalition."
Despite giving conditional support to net-zero carbon emissions by 2050 under Scott Morrison's prime ministership, Mr Joyce has been a strident critic of Labor's net-zero policies and the push to shift Australia's economy to renewable energy.
Dr von Strokirch, who is based in Mr Joyce's electorate, said it was "very odd, perhaps even somewhat unethical" for him to leave the party so soon after being re-elected.
"He's just going to sit there, even though he was elected on the platform of the National Party," she said.
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