The Victorian senator resigned from the party on Saturday, claiming he had not been afforded procedural fairness over misconduct claims, but will remain in parliament.
In a letter to Victorian Liberal Party president Greg Mirabella seen by AAP, Senator Van said he could not remain a member of a party that "tramples upon the very premise on which our justice system is predicated".
"Given the Liberal Party's wholesale disregard for due process and natural justice in relation to allegations made against me, I write to resign my membership effective immediately," Senator Van said in the letter.
It followed bombshell allegations made last week by independent senator Lidia Thorpe and former Liberal senator Amanda Stoker, who both alleged Senator Van touched them inappropriately previously.
Senator Van denied the allegations and said he would co-operate with any investigation.
Opposition Leader Peter Dutton removed Senator Van from the Liberal party room last week and called on him to resign from the Senate.
On Friday, Mr Dutton confirmed further allegations had been brought against Senator Van.
Senator Van said he was "deeply distressed and hurt that I have not been afforded procedural fairness" in relation to the allegations against him.
"I have worked tirelessly for the party and fought hard for its beliefs over many years," he said in the letter to Mr Mirabella.
Nationals leader David Littleproud said he was shocked by the allegations made against Senator Van.
"I appreciate Senator Van wants to have a presumption of innocence, but I also appreciate the fact that Peter Dutton has the right to protect the Liberal Party and to undertake his own investigation," he told Nine's Today program on Sunday.
"If his behaviour doesn't meet the standards of the Liberal party, then (Peter Dutton) has every right to remove Senator Van from his party room, and the Liberal Party has every right to accept his resignation."
Mr Littleproud hit out at Senator Van's decision to remain in parliament on the cross bench.
"While the senator can stay, under the law, really, he wasn't elected on his own volition," he said.
"He was elected on the Liberal Party. He wants to remove himself from the Liberal party, and then he should probably also remove himself from the Senate."
Indigenous Australians Minister Linda Burney said the events of parliament in the past week sent a bad message to the public.
"(Parliament House) should be a safe place to work, the parliament of any workplace in Australia should be safe," she told Sky News.
"Clearly there are still issues, but I do not take away from the fact that much good work (on implementing reforms on workplace culture) has been done."
Senator Van's resignation came a day before the Victorian Liberal Party's administrative committee was due to meet to further consider the allegations.
He was sworn in as a federal Liberal Party senator for Victoria in July 2019.
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