Western Australian Senator Jordon Steele-John made the shock move on Thursday after seven Greens members wrote a letter demanding an investigation into the alleged conduct.
The 32-year-old upper house member is accused of concerning behaviour in the presence of women from 2017 to 2025.
Senator Steele-John said the allegations were made without specifics.
"I utterly reject this characterisation of me, which tries to assert I am someone I am not," he said in a statement.
"Any allegation of this nature is extremely serious and must be treated accordingly.
Greens leader David Shoebridge said he first received word of complaints against Senator Steele-John in a letter from the seven party members on Tuesday night.
The party took the claims "incredibly seriously", he told reporters in Canberra on Thursday.
He did not stipulate whether he had heard allegations or rumours about the WA senator's behaviour before taking the party's top job on September 30.
"I received the correspondence in my capacity as leader of the Australian Greens and I've dealt with it with the urgency which I think is appropriate," Senator Shoebridge said.
But a source inside the youth wing of the party's NSW branch told AAP Senator Steele-John had been raised in connection with allegations of sexual harassment as early as October 2018.
At the time, a general meeting of the state's Young Greens directed their national delegates to block and indefinitely delay motions to formally investigate the WA senator for alleged sexual harassment.
In the same meeting, they also asked the delegates to keep voting to block Senator Steele-John appearing on the party's social media pages.
Both motions were agreed to by consensus, the source said, and are the only times the WA senator's name appears in NSW Young Greens meeting minutes since before he entered the federal upper house.
Senator Shoebridge, who was a member of the NSW Legislative Council at the time, on Thursday said he did not remember any NSW Young Greens motion relating to Senator Steele-John.
"I was in a different parliament. I do not recall having any involvement at all in that, and and I don't think people would expect an upper house MP in the state parliament to have any role in that," he said.
Senator Shoebridge maintained he was only told about the allegations on Tuesday and accepted Senator Steele-John's leave of absence Thursday afternoon.
Tuesday's letter, extracts of which have been published by the Nine newspapers, said multiple female party members were warned not to be alone with Senator Steele-John because of the allegations against him.
"These warnings have come from inside and outside the party, demonstrating that knowledge of his alleged reputation extends beyond party membership and out into the community," it read.
"There are multiple others who were too fearful of backlash by Senator Steele-John and others in the party to sign on."
The WA senator will self-refer matters outlined in the letter to an independent complaints process overseen by that state's party wing.
Senator Steele-John entered parliament in 2017 when he was 23, which at the time made him the youngest senator on record.
He is the party's spokesman for disability and mental health, leading a campaign against NDIS cuts.
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