Dr Ian Campbell, a GP who has been instrumental in pushing the issue of obesity up the political agenda, resigned as president of the National Obesity Forum last month.
But Dr Colin Waine, the chair of the forum, said there were other reasons involving the relationship between Dr Campbell and the former chief executive, Felicity Porritt, who left the charity in November.
Waine claimed the two were in a relationship when she was appointed and that Campbell had failed to tell the trustees about it. "Much to our dismay, that relationship was not declared openly," he said.
But Campbell said this was "a complete and utter lie", and insisted Porritt was appointed in April 2005, when he was president but not a trustee.
Campbell said that the trustees knew of the relationship when the appointment was made and, although he took part in a group interview, he took no part in the subsequent decision to appoint her.
Campbell said Porritt, his established partner, was brought in to broaden the funding base of the charity and was made redundant only months after her appointment because the charity did not like what she was trying to do.
But Waine said there had been no conflict over her desire to broaden the funding base of the charity.
Campbell insisted that his core reason for leaving was the growing influence of the drug companies.