Japan's transport ministry has started a special audit of the operator of a tour boat that went missing off the northernmost prefecture of Hokkaido.

Four ministry officials began the investigation at the office of Shiretoko Pleasure Boat on Sunday evening.

The company's 19-ton ship, Kazu One, went missing on Saturday during a cruise off the Shiretoko Peninsula. It was carrying 26 people.

The ministry says the boat hit a floating object in May last year, injuring three passengers, and ran aground the following month. It says the operator submitted a report on its improvement measures to the government after the two accidents.

The ministry says it is a serious matter that the same boat was involved in another accident.

Officials will look into whether the company operated the boat in accordance with the law and if appropriate maintenance was carried out. They will also interview company officials.