Nigel Griffiths, the deputy leader of the Commons, left the government yesterday in protest at the decision to renew the Trident nuclear weapons system.

After delivering a letter to the Prime Minister in Downing Street, the MP for Edinburgh South, said he was resigning with a heavy heart but a clear conscience. He will make a fuller statement in the Commons later this week.

Ever since Gordon Brown battled to keep Mr Griffiths in the government, albeit in an unpaid job, he has been regarded as an ally of the Chancellor but last night government sources distanced Mr Brown from the resignation.

"This isn't done with Gordon's say-so. Nigel has always overplayed his relationship with Gordon and it is unlikely that he would have tried to change his mind," he said.

Other colleagues wondered if Mr Griffiths, whose parliamentary majority was only 405 at the 2005 general election, had his eye on his electoral fortunes when he promised constituents that he would resign.

Ian Murray, an Edinburgh councillor whose Alnwickhill ward is in Mr Griffiths' Edinburgh South constituency, said: "I think it was a very courageous and brave decision for him to resign over the issue. A lot of us that are in the constituency, and certainly a lot of the constituents I speak to on the doorsteps, can't understand in this day and age of us trying to be more conciliatory, why we need to replace Trident."

Mr Griffiths is one of 12 Scottish Labour rebels over the replacement of Trident but the government, to the dismay of the leadership, will win the vote with the help from the Tories.

Senior cabinet members acknowledge that it is a difficult decision, but they believe it is the right thing to do for the country's security and think that by having to rely on Tory votes makes them vulnerable on security issues.

Last night fellow rebels rallied to support Mr Griffiths. Jeremy Corbyn, the Labour MP for Islington North, said he admired his stand, while Alan Mackinnon, chairman of Scottish CND, said: "We welcome the stand taken by Mr Griffiths on this issue and we hope his example will be followed by other Labour MPs."

The government is planning to acquire four new submarines, at a cost officially estimated at £15bn to £20bn, though Mr Blair has said the fleet could be cut to three if technological developments allow maintaining continuous at-sea patrols with fewer vessels.