The director of the National Gallery, Charles Saumarez Smith, has announced he is leaving the gallery to take up a newly-created post as secretary and chief executive at London's Royal Academy. No reason was given for his resignation only five years into a contract that would have lasted until he was 65.

But there has been widespread media speculation that Saumarez Smith, 53, became wearied by an ongoing dispute with National Gallery chairman Peter Scott. Scott issued a statement last month saying: 'Charles Saumarez Smith has enjoyed five years of remarkable achievement.'

At the time of going to press, Saumarez Smith was negotiating the timing of his departure with the board, which is believed to be this autumn.

Saumarez Smith's announcement comes barely a month after Roy Clare, the director of the National Maritime Museum, announced his departure to 'pursue a new opportunity within the heritage sector'.

A spokeswoman for the museum said that, 'he felt it was a good time to leave on a high with the opening of the Time and Space gallery [at the Royal Observatory]', in the same month. However, sources say that Clare had also had a long-running disagreement with his chairman. And there are rumours of difficulties at other museums, particularly National Museums Liverpool.

Museums Journal has also learned that at the end of March there was a meeting of chief executives of most of the department for culture's non-departmental government bodies (including national museums and other arts and heritage organisations) at which governance was discussed. A number of people expressed concerns about the way the trustee and governance system is running.

This is not the first time that differences between museum boards, chairs or directors has led to a director's departure. In 2005, Lindsay Sharp resigned from the Science Museum; Alice Rawsthorn stepped down from the Design Museum in 2006; and in 2001 Alan Borg left the Victoria and Albert Museum.

According to sources close to national museum directors and boards, part of the problem is the lack of any satisfactory mechanism at the department for culture to resolve disputes between directors and chairs.

In at least two recent cases it is believed that the directors and chairs had fundamentally different ideas about the future direction of the museums and their audiences.

While directors, as accounting officers, have a range of performance targets they must meet to satisfy the department for culture, the terms of trustees' behaviour and responsibility are much less clear. 'The big question is who governs the governors,' one source told Museums Journal.

Another remarked: 'There seems to be a shift, with boards moving from an advisory and supporting role to one that is more to do with performance management.

The trouble is that seems to be combined with the attitude that there's plenty of good director material so they are quite willing to look to replace directors, rather than resolving differences in an open and frank way.'

A spokeswoman for the Department for Culture, Media and Sport denied that there was no mechanism to resolve disputes, saying that in the case of national museums, the head of the museum unit, Ben Cowell, would be consulted. 'It isn't down to us to arbitrate in arguments between two individuals because museums and galleries are independent,' she said.

But a national museum trustee said: 'There are a whole range of issues. Sometimes boards intervene because the executive is not competent. But sometimes trustees, especially from business, seem to leave their normal common sense behind the minute they do something in the cultural field.

In general, there is a big issue about the lack of trustee and chair training and development. The problem is, once trust breaks down between a director and chair, wherever it starts, the situation has a nasty habit of unravelling quickly.'

Jane Morris