In a statement, the Foreign Ministry said Foreign Minister Datuk Seri Anifah Aman conveyed the decision to his New Zealand counterpart, Murray McCully, Wednesday.
"The Government of Malaysia's decision is a clear testament of the excellent bilateral relations between Malaysia and New Zealand," it said.
The statement said Second Warrant Officer Muhammad Rizalman Ismail, a former Defence Staff Assistant at the High Commission, would be accompanied by a senior military officer from the Defence Ministry.
"Malaysia has complete faith in the New Zealand legal system and has full confidence that Muhammad Rizalman will be given fair treatment with dignity as provided under the law," it said.
The Ministry said the Malaysian Government was of the view that this decision would provide an opportunity for Muhammad Rizalman to cooperate fully and assist the New Zealand authorities in the on-going investigation into the allegations made against him.
"In this regard, the legal principle that one is considered innocent until proven guilty should apply to Muhammad Rizalman. The Government of Malaysia will provide legal assistance to him if necessary," it said.
Muhammad Rizalman, 38, was arrested in New Zealand on May 9, and brought to court the following day to face charges of burglary and assault of a young woman with intent to commit rape.
Anifah told a press conference on Tuesday that Muhammad Rizalman and his family returned to Malaysia on May 22, with the agreement of the New Zealand side.
He had said that during a discussion on the matter between Malaysian and New Zealand officials on May 12, the New Zealand side had offered an alternative for the accused to be brought back to Malaysia.
McCully reportedly said that there may have been ambiguity in communications between the two countries in dealing with the case.
He also said that he had already apologised to Prime Minister John Key for not having the latter briefed thoroughly on the case before Key decided to speak publicly on the matter.
"I told the Prime Minister (Key) that he had not been given all the information he should have been given.
And I have taken responsibility for that and apologised to him.