Senator Van resigned from the party following allegations of inappropriately touching independent senator Lidia Thorpe and former Liberal senator Amanda Stoker.
Parliament will meet on Monday for the final sitting week before a six-week winter break.
Opposition Leader Peter Dutton had called for Senator Van to resign from parliament altogether, but the Victorian senator quit the party before a committee could meet to discuss the allegations against him.
Mr Dutton said there were also allegations from a third person against Senator Van.
Senator Van said in a letter to Victorian Liberal Party president Greg Mirabella 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,” he said.
Nationals Leader David Littleproud said Senator Van should be afforded the presumption of innocence, but Mr Dutton reserved the right to remove him from the Liberal partyroom.
“In the Senate there’s a clearer case around where senators remove … themselves voluntarily out of that party, and they were elected within that ticket, then they should be replaced with someone from that party,” he told ABC Radio on Monday.
Agriculture Minister Murray Watt said the previous week in parliament when the allegations were raised publicly was distressing.
“They are very serious allegations, and (Senator Van) should really seriously consider his position,” he said.
“It is a matter for David Van and the Liberal Party as to how they handled these allegations when they were first raised and what efforts were undertaken.”
Despite the allegations being raised, Senator Watt said the workplace culture had improved.
Nationals senator Bridget McKenzie said on Sunday she was aware of rumours in parliament about Senator Van but did not know the specific allegations made against him.
She said the decision by Mr Dutton to immediately expel Senator Van from the party room in the wake of the allegations was the right one.
“All political parties have faced these type of internal challenges over the recent past and for a leader to be so decisive, I think, was a testament to his strength of feeling around these matters,” she told ABC’s Insiders on Sunday.
“I think there was a lot of cheers silently across parliamentary offices with such decisive action being taken by a leader.”