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In a statement to RNZ, the man said he had made the difficult decision to resign because of stress and to avoid being a distraction.
"I have enjoyed my time working in Parliament, but today have made the very difficult decision to resign because of the stress of the situation, and my wish not to be a distraction to the work of the Government," he said.
"I adamantly refute the serious allegations made against me. I co-operated fully with the initial inquiry."
The man said he was now taking part in the new review of the whole complaint process and would continue to do so, "having been assured that this process will be fair to all parties".
In a separate statement, his lawyer Geoff Davenport said his client was adamant the reported claims were "without foundation" and had been cleared by Labour's initial investigation.
His client was in the "distressing situation" of now being subject to a further inquiry and extensive media coverage, he said.
"The toll that is being taken on him is severe."
Mr Davenport said he had advised his client that it would be "completely inappropriate" to litigate the matters in the media and would not be doing so.
Claims of bullying, harassment and sexual assault were first reported about five weeks ago.
Labour had launched an internal investigation into seven formal complaints about the staffer's behaviour, and ultimately concluded that no disciplinary action was warranted.
That decision is now being reviewed by Maria Dew, QC, after the complainants approached media and National Party deputy leader Paula Bennett with concerns about the complaints process.
Prime Minister Jacinda Ardern has declined to say which senior Labour Party figures told her there was no sexual assault complaint.
She has told RNZ's Checkpoint programme tonight she did not want to pre-empt the external inquiry now under way.
Ms Ardern said she had personally apologised to the complainants.
Ms Ardern has repeatedly stated that the man's employer - Parliamentary Service - was unable to take any action as it had received no formal complaints from other staff members.
Senior Labour MP and minister Grant Robertson maintained he had acted appropriately throughout the sexual assault investigation into complaints against the Labour staffer.
Correspondence seen by RNZ shows Mr Robertson had been aware of some of the allegations over the past few weeks.
He told Checkpoint today he was distressed to read the allegations on the website the Spinoff, which he had never seen before.
"We've heard from the prime minister this week about what she said, about the fact that at every stage of this process, whenever concerns have been raised, they've been referred to the party to ensure that they were being acted on appropriately - that is the same experience for me."
Mr Robertson would not comment on whether the prime minister had a conversation with him about what he knew.
The man has been working away from Parliament's precinct for the past five weeks.