Japanese rescuers have located the hull of a tour boat off the country's northern coast, six days after the vessel disappeared in an accident that killed at least 14 people.

The hull of Kazu I was found on the seabed at a depth of about 120 metres off the northern island of Hokkaido in pitch-dark waters, Japan's coast guard said.

The boat had departed for a tour of the peninsula, which is known for its rugged coastal scenery and wildlife, with 26 people on board, including two crew and two children.

The two crew of the boat sent a distress call on Saturday afternoon, saying the vessel was sinking.

The boat was located near Kashuni Waterfall, known to be a difficult place to manoeuvre boats due to the rocky coastline and strong tide.

Fourteen people have been confirmed dead, including a child. Twelve people remain missing.

The bodies were found in the same area near the tip of the peninsula, about 14 kilometres north of where the boat sent its distress call.

Japan's coast guard said some of the bodies that had been recovered were without life vests, despite officials saying they had been told by the operator that all passengers on board had been wearing flotation devices.

The coast guard said a Russian guard ship lost sight of someone wearing a life jacket who was adrift at sea in waters west of an island known as Kunashiri on Wednesday afternoon. 

The island, known in Russian as Kunashir, is one of four islands north of Hokkaido that are at the centre of a territorial row between Tokyo and Moscow, after they were seized by the Soviet Union at the end of World War II.

Japan's transport ministry is investigating the boat's operator, Shiretoko Pleasure Cruise, which had two accidents last year.

Last May, a boat belonging to the company collided with an object, causing three passengers to receive minor injuries.

In June, a boat ran aground but no-one on board was injured. The incident involved the same captain of the sunken Kazu I. 

Shiretoko Pleasure Cruise was instructed to improve its safety after the two incidents.

The ministry said it was looking into safety standards and the decision to conduct the tour on Saturday despite the rough weather.

Earlier this week, Japan's coast guard said it was gathering evidence toward making a criminal case on suspicion of professional negligence.

"We will thoroughly investigate what caused this situation and what kind of safety oversight was involved to allow the tour in order to prevent another accident," Japan's Transport Minister Tetsuo Saito said on Monday.

A tour boat crew belonging to another operator told Japanese broadcaster NHK they had warned the Kazu I crew of rough seas in the area and told them not to go.

They also said the same boat ran aground last year and sustained a crack on its bow.

The cause of the accident remains under investigation, but experts suspect the boat ran aground and was damaged before it sunk.

ABC/Reuters