This morning Dr Mapp said he had briefed about the situation and regarded it as a significant issue because of the seniority of the person.
"But there is an investigation being held and I don't intend to prejudge the outcome of that."
Asked if he thought there was an issue with drinking in the military, Dr Mapp said: "Well there are 10,000 people in the Defence Force. They tend to be at the younger end of the spectrum. It probably reflects a bit of a cultural issue that New Zealand as a nation actually has."
He had had discussions with the Chief of Defence Force over the years on the same issue because it came up from time to time.
A Defence spokesman confirmed that the Navy had "relieved one of its ships' captains of his duties" while the allegations were investigated.
"The allegations are not of a criminal nature and at no time was the ship or its company put in any danger," Defence Force spokesman Chris Wright said.
He said details of the allegations would not be made public until it was decided whether charges under the Armed Forces Discipline Act will be laid.
But a Navy source told the Herald the disciplinary action against Commander Butcher was common knowledge among crew members.
"To relieve a guy of his command is probably the biggest embarrassment a person can get... that's a real big no no," the source said.
Commander Butcher joined the navy in 1989 and has had a long and decorated career.
He was appointed a member of the New Zealand Order of Merit in the 2006 New Year Honours List for services to the New Zealand Defence Force and his work as the navigation training officer.
In 2006, he attended the United States Naval War College in Newport, Rhode Island, and three years later was appointed military assistant to the Chief of Navy and confirmed in the rank of Commander.
Commander Butcher was appointed captain of Te Mana and its 178 officers and ratings in August last year.
At 118m long and weighing 3600 tonnes, Te Mana is one of the navy's two ANZAC Class frigates, and considered one of the main fighting units.
Its role is to protect New Zealand and its maritime resources, participate in UN missions, and provide support for civil defence and search and rescue operations.
As part of a recent five-month deployment, Te Mana visited Ho Chi Minh City and was at an international fleet review to celebrate the golden jubilee of the Royal Brunei Armed Forces during a visit to Brunei.
In the fleet review, 16 warships from 13 nations sailed in formation, watched by the Sultan of Brunei and 11 navy chiefs, including Rear Admiral Tony Parr from New Zealand.
The ship also exercised with the Indian naval vessel INS Kesari.
Performing drills with the Indian warship was a valuable opportunity for the navy, said Commander Butcher.
The name Te Mana means "status" or "authority" in Maori, and the ship's motto is "Kokiri Kia U" - "Striving towards perfection".
The investigation is the latest in a string of embarrassing alcohol-related incidents involving the Navy.
Most recently, a petty officer drank up to 17 beers and cycled away from his ship while he was supposed to be on guard duty.
Norman Anderson appeared at a court martial at the Devonport Navy base in June and pleaded guilty to five charges including leaving his post, drinking while on duty and stealing food from the ship's stores.
Contact: newsdesk@nzherald.co.nz