The fresh allegation was made public on the same day Senator Van was dumped from the opposition party room following allegations made by Senator Thorpe in parliament.
Ms Stoker's allegations referred to an incident in November 2020, where she said the Liberal senator inappropriately touched her at an informal social gathering at Parliament House.
"He did so by squeezing my bottom twice. By its nature and by its repetition, it was not accidental. That action was not appropriate. It was unprofessional and uninvited," the former Queensland senator said in a statement.
"I raised the matter with Senator Van at a meeting the following day. I described the action, told him it was unacceptable, and that it was not to be repeated."
Ms Stoker said she held a meeting following the alleged incident and had accepted Senator Van's apology.
She said while she wanted the incident to be kept confidential, she said that view was "no longer tenable" in the wake of Senator Thorpe's statement.
Earlier on Thursday, Opposition Leader Peter Dutton said he had told the Victorian senator earlier on Thursday he was no longer welcome in the party room.
Mr Dutton said further allegations had been made against Senator Van since Senator Thorpe's original claims were aired.
It followed a speech by Senator Thorpe to the upper house on Thursday in which she detailed allegations of sexual assault by a Liberal senator.
She had under parliamentary privilege on Wednesday accused Senator Van of harassment and sexual assault.
Senator Van has rejected Senator Thorpe's claims.
While not naming Senator Van in her speech on Thursday, Senator Thorpe said she was followed and then cornered in a stairwell by a senator at Parliament House, before she was "aggressively propositioned and inappropriately touched".
"There are different understandings of what amounts to sexual assault ... to me, it was sexual assault," she told parliament.
"I was afraid to walk out of the office door.
"I would open the door slightly and check the coast was clear before stepping out.
"It was to the degree that I had to be accompanied by someone whenever I walked inside this building."
Senator Thorpe said she would not pursue legal action over the incident or go to the police with the claims.
The independent senator said the incident was not isolated and there were other people in parliament who had inappropriately touched her.
Senator Van told parliament on Thursday Senator Thorpe's allegations were "concocted from beginning to end".
"Nothing that she has alleged of me is truthful," he said.
"No such exchange occurred between us.
"There is no interaction that could conceivably resemble what she described today.
"Making false allegations in the Senate today is disgraceful and brings the Senate into disrepute."
But he accepted he would no longer sit in the Liberal party room.
Senator Thorpe made the initial accusations of Senator Van on Wednesday while he was making a speech accusing the Labor Party of unethical behaviour in its handling of the Higgins sexual assault allegations.
Senator Van said he had accepted an offer made by then-Senate president Scott Ryan in 2021 to move to an office further away from Senator Thorpe.
He had done so in the wake of a claim - which he rejected - that his proximity to her office made her feel "uncomfortable".
In a statement, Senate President Sue Lines said she had heard the request for more security and greater CCTV in parliament.
"I will raise the proposal with the Speaker of the House as we have a joint responsibility for the building," she told the Senate.
Senator Lines also said the statement made by Senator Thorpe on Thursday did not breach any parliamentary rules.
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