Lidia Thorpe accused Liberal Senator David Van of sexually assaulting her, during parliamentary proceedings on Wednesday, before returning to the senate to withdraw her comments hours later.

The allegations came during a debate in the Senate as Senator Van criticised Labor's handling of Brittany Higgins' alleged sexual assault during discussion of the Sex Discrimination Commissioner's report on parliamentary workplaces.

The Gunditjmara, Gunnai and Djab Wurrung senator interjected a number of times before making allegations against Senator Van.

"I'm feeling really uncomfortable when a perpetrator is speaking about violence.

"I can't (withdraw), because this person harassed me, sexually assaulted me. And the Prime Minister had to remove him from his office," she said when first asked to withdraw the comments.

"To have him talk about this today is an absolute disgrace."

On Thursday Senator Thorpe said: "Yesterday I made remarks in relation to another senator. I then had to withdraw them because the rules of the Senate do not allow you to speak about someone's character, only about something they have said."

Senator Van denied the allegations.

"I utterly reject that statement, that disgusting statement outright. It is just a lie. And I reject it … it's just not true."

Deputy Senate President Andrew McLachlan, who was overseeing the chamber, asked Senator Thorpe to withdraw her comments which were "inappropriate and reflected poorly on the member".

The comments were referred to the Senate President.

Senator Thorpe's allegations are understood to be in relation to an alleged incident in 2021.

In March she alleged she had been sexually assaulted and harassed multiple times by both Labor and Coalition MPs within her first six months in parliament. At the time Senator Thorpe didn't identify individuals.

Senator Van later released a statement again rejecting the allegations.

"In the Chamber today Senator Thorpe made unfounded and completely untrue allegations against me that I immediately and unequivocally denied and continue to deny," he said.

"These outrageous and reprehensible comments were made by Senator Thorpe using parliamentary privileges in the most malicious and despicable way.

"My lawyers have written to her already making my position clear in the strongest possible terms."

At 7:30pm Ms Thorpe addressed the chamber to withdraw her earlier comments.

"President, earlier today I made some comments in relation to another senator. The Deputy President referred the matter to you, and you requested me to withdraw those remarks," she said.

"In order to comply with the parliamentary standing orders, I withdraw those remarks. For the information of the Senate, I will make a further statement on the matter tomorrow. Thank you."

This story was updated at 1pm WST on Thursday 15 June.