Mr Ishiba (centre) has admitted the ministry's handling of the inquiry had flaws, but denied any attempt to hide information and pledged to resign if a cover-up was shown to have taken place. -- PHOTO: AFP

He visited the family in Chiba prefecture, east of Tokyo, amid growing calls for the resignation of Defence Minister Shigeru Ishiba and allegations that top officials have tried to cover up what happened.

Mr Fukuda met with the relatives of the fishermen, a father and his adult son, who have been missing since the early morning of February 19, when the Atago destroyer crashed into their tuna-fishing boat.

He was moved to tears as he looked at photos of the men at their house, and he apologised to their family and promised to prevent similar accidents, according to people who witnessed the visit.

Mr Fukuda later met with reporters in Tokyo and said the family wrote him a letter urging him not to dismiss Mr Ishiba and other senior officials connected to the incident.

'The letter said that Minister Ishiba, the captain of the ship and others should not just quit and end their involvement in this. It said, rather they should stay and continue to work to prevent accidents like this and educate young people,' Mr Fukuda told reporters.

'I want the Defence Ministry and the Self Defence Forces to be truly trusted by the public. To realise that goal, we must reform the organisation,' he said.

Mr Ishiba and the destroyer's captain called on the family earlier in separate visits.

The coast guard terminated the search for the fishermen on Sunday, following calls by their family to end the effort.

The fishing village ended its own search efforts last month and held a ceremony at a local port to pray that the missing fishermen would rest in peace.

'It has been 13 days since the accident. Considering the weather and other conditions, we have judged that the possibility of their survival is extremely low,' the coast guard told local reporters, according to Jiji Press.

The Atago is equipped with the Aegis radar combat system, seen as a frontline defence against rival North Korea.

The opposition has alleged an attempted cover-up in the incident because the defence ministry flew the Atago's duty officer to Tokyo for questioning before an official probe was opened.

Mr Ishiba has admitted poor judgement in interviewing the officer but said it was not his decision to do so.

Japan, officially pacifist since World War II, only created a full-fledged defence ministry last year, which has since been beset by scandals. The ministry's former top bureaucrat was arrested last year for allegedly taking tens of thousands of dollars worth of bribes. -- AFP