Mr Clements quit the role protesting his innocence and denying the latest allegations against him by 27-year-old staffer Stefanie Jones aired in a newspaper interview on Thursday.

Ms Jones alleged Mr Clements – who is married with three children – became upset last year after she said she intended to tell her fiance, state Labor organiser David Latham, of an affair she and Mr Clements had had some years earlier.

She claimed Mr Clements locked the door of the Parliament House office they were in, demanding a guarantee from her that she wouldn't disclose the affair and aggressively told her to kiss him.

Ms Jones also blasted the ALP's treatment of women.

"There's such a lack of support ... as long as the party has people like [that], the filth ... the continuation of disgusting treatment of women will continue," she said.

"I would say if you're a woman in the Labor Party be careful."

In his resignation statement, Mr Clements said this version of events was "completely false."

"This matter was the subject of a thorough police investigation and a separate independent investigation conducted on the balance of probabilities, neither of which resulted in any charges or findings of wrongdoing on my part."

But his fate was all but sealed when federal Opposition Leader Bill Shorten announced on Thursday morning that he had asked for an urgent report on the matter.

"We have no tolerance for workplace harassment and I do expect this matter to be now resolved, full stop," Mr Shorten said.

Within hours, acting Labor leader Linda Burney had called for Mr Clements to go after consulting NSW Opposition Leader Luke Foley, who is on leave.

Fairfax Media has confirmed that Mr Clements met Ms Burney on Friday last week to discuss the matter, which had become the subject of an apprehended violence order application and was settled in a court hearing this week.

At the Wednesday hearing police withdrew the AVO application. Mr Clements agreed to several undertakings on a no-admissions basis. He was never charged with an offence, and disputed the allegations.

However, he agreed to not approach Ms Jones for 12 months and to not apply for an unrestricted pass to the NSW Parliament. This meant he would need to be signed in and accompanied at all times.

At their meeting last Friday Ms Burney urged Mr Clements to agree to the undertakings, suggesting it would be good for him, his family and for the party.

But on Thursday, following Mr Shorten's announcement, Ms Burney declared Mr Clements' position as general secretary "untenable".

"It has now become clear that this matter will only be resolved with the resignation of Mr Clements," she said.

Ms Burney said it had become "an issue of confidence in Mr Clements [and] the views of party members. It has also become an issue in making sure we have a viable, properly operating division in Sussex St".

She said the party needed to "draw a line under this matter" before next month's NSW Labor conference and the federal election due this year.

Mr Clements said he agreed to undertakings "in order to spare the party, my family and all those involved, a difficult and traumatic legal process. Those undertakings were made on a strictly no-admissions basis."

"Throughout this process I have maintained a dignified silence. I am disappointed that others chose not to – instead using the media to pursue their agenda."

Mr Clements – who earns about $200,000 a year in the job and had four years remaining on his contract – had been rumoured to be trying to negotiate a payout as high as $1 million. But party sources said this was a wildly inaccurate figure.

He is likely to be replaced by the current Right faction assistant secretary, Kaila Murnain​.