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"If it comes to a stoush between Trevor Mallard and Hekia Parata I know who I'd believe -- it certainly wouldn't be Trevor Mallard," he said.
The issue was raised at the education select committee when it was looking at future spending.
Mr Mallard asked Ms Parata if she had ever hit a staff member.
She vehemently denied it and said she was offended by the question.
Outside the committee, she said: "I can tell you categorically that I have never hit a staff member in my current employ or in my previous employ.
"I think it is really inappropriate, offensive and inaccurate."
She said she was "aware there has been a rumour but there is no substance to it".
Mr Mallard told reporters after the committee that he believed a former staff member had left the office after being hit on the head. He said he had heard the allegation indirectly from "a very good source".
Speaking in Tonga yesterday, Mr Key said he accepted the word of his minister and she had said it did not take place. "She is not going to lie to a select committee."
Ministerial Services, which employs ministerial office staff, would not say if any former staff member of Ms Parata's claimed to have been hit. But it said that there had been a personal grievance from one of the staff who was employed in her office.
- Audrey Young of the New Zealand Herald