Mr Joyce has not directly told Prime Minister Malcolm Turnbull he is resigning, but he said he spoke to Mathias Cormann, who is acting in the role while Mr Turnbull is overseas.
Mr Joyce has been in the spotlight following revelations of his affair with his former adviser and now pregnant lover Vikki Campion and allegations he created a number of high-paying jobs for her.
"Any allegation of sexual harassment is a very serious allegation".
Prime Minister Malcolm Turnbull who is now in the US for a four-day trip to hold talks US President Donald Trump also deflected question on his deputy when he addressed media outside the White House.
Barnaby Joyce has been embroiled in scandal.
"He said allegations of wrongdoing should be immediately referred to police so that the veracity of any claim could be properly tested", the spokesman said.
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Broad's intervention came before the party confirmed late on Thursday it had received a formal sexual harassment complaint against Joyce.
FLYNN MP Ken O'Dowd has refused to be drawn on how he plans to vote if National Party leader Barnaby Joyce is challenged on Monday.
Barnaby Joyce, Australia's Deputy Prime Minister and Minister for Agriculture and Water Resources, stands in a paddock on a property on the outskirts of the township of Merriwa, located north-west of Sydney, in the electorate of New England, in Australia, March 29, 2016.
"I've been at great pains to stress that I have not, nor has my Party, sought to influence in any way, the deliberations of the National Party, any more than I'd expect the National Party to seek to influence deliberations of the Liberal Party". "All complaints are taken seriously and treated with strict confidentiality and given due process".
Joyce said he'd return to the backbench but would definitely contest his seat at the next election, saying that he never claimed to not be "rough around the edges" but that he was dedicated to improving the lives of people who may not have inherited wealth, been born to the "best family" or had access to an excellent education. "I understand that complaint is being investigated", Mr Cormann said.
"It is the view of the Parliamentary National Party of Western Australia that Mr Joyce's position as a Federal Leader is no longer tenable".
"The leadership of the National Party, is a matter for the National Party", Mr Turnbull said.