Ministerial aide Jim Devine has become the second member of the government to quit over plans to renew the UK's Trident nuclear weapons.
Jim Devine is expected to vote against the government
The Livingston MP quit his job as a parliamentary private secretary at the Department of Health.
Deputy Commons leader Nigel Griffiths quit on Monday in protest at Trident.
Although a Labour rebellion is expected in a vote on Wednesday, the Conservatives back renewal of Trident, making a government defeat unlikely.
It is understood Mr Devine hopes to speak during Wednesday's Commons debate on replacing the submarine-based weapons system, at an estimated cost of up to £20bn.
Mr Devine, 53, became an MP after winning a by-election prompted by the sudden death of former foreign secretary Robin Cook in 2005.
Previously he had been Mr Cook's election agent and was chairman of the Scottish Labour Party in 1994/95.
He did not receive a salary for his post as parliamentary private secretary.
Ministers say the long lead time in developing and building the replacement submarines means a decision needs to be taken soon on replacing Trident.
Ahead of the Commons vote Conservative leader David Cameron made clear his support for the plans on BBC Radio 4's Today programme on Monday.
He said: "I think it needs to be done and I've always supported Britain having a nuclear deterrent, so when Trident comes to the end of its life it needs to be replaced."
The Liberal Democrats say Britain's stockpile of warheads should be cut by 50% but a decision on replacing them should be delayed until at least 2012.
The Lib Dems will vote against the government's proposals on Wednesday, joining as many as 100 Labour MPs who also oppose renewal.
Announcing his resignation on Monday, Mr Griffiths, MP for Edinburgh South, said: "I'm resigning with a heavy heart but a clear conscience.
"I intend to make a personal statement in the House of Commons to colleagues and it is only right that they hear the reasons first."
Labour MP Stephen Pound, a ministerial aide to party chairman and deputy leadership contender Hazel Blears, is also thought to be considering his position.