In a statement to Fairfax, Sir Owen denied the allegation. He said he regretted not taking the matter to court, but had decided after two years of dispute to resolve the case to avoid further "horrendous court costs" and to bring the matter to an end.
"It saddens me that yet again it appears the New Zealand media is delving into my personal life to fill their pages while New Zealand is ranked the third highest country in the world for rape and this issue goes virtually unreported."
The court documents reportedly show the charge was dismissed in August 2004 following a six-month period of probation.
Sir Owen has since signed two declarations that he has no history of violence towards women or children - one for the Glenn Inquiry, which has been shaken by resignations, and one for the White Ribbon anti-violence campaign, for which he has applied to become an ambassador.
The founding director of the $2 million Glenn Inquiry, Ruth Herbert, resigned in May, which was followed by a number of other resignations.
The inquiry board's chairman, Bill Wilson QC, told Radio New Zealand he had been informed about what had happened in Hawaii.
He said he was confident there was nothing to the abuse allegations and it was not surprising the charge was was dismissed.
Mr Wilson said the inquiry members were confident Sir Owen's declaration was accurate.
White Ribbon campaign manager Rob McCann initially told Fairfax Media it had not been aware of the charge, but said today said it was aware of the charge and would consider it in Sir Owen's application to become an ambassador.