Tony Blair and Gordon Brown suffered the largest non-Iraq related revolt of the Labour Government last night when nearly 100 MPs opposed an immediate decision to renew the Trident nuclear missile system.

Despite last-minute concessions and a massive effort by the whips to rally support, in which Mr Brown became heavily involved, 94 Labour MPs joined the Liberal Democrats and nationalist MPs in calling for a delay. Then 87 Labour MPs rebelled once more, voting directly against a motion to update Trident. The revolts came despite warnings from senior Labour figures that the party risked appearing to have reverted to “old Labour” ways.

Mr Brown was anxious to contain the rebellion to inject a new sense of discipline into the Labour ranks before his expected takeover as leader in the summer.

The scale of the revolt is a big embarrassment for both men, and confirms that Mr Blair’s authority has all but disappeared. A senior whip told The Times that the revolt would have been even bigger but for Mr Brown’s influence on his own close supporters.

Without Tory backing the Government would have easily been defeated, a factor that will be used heavily against Labour in the run-up to the next election. Despite the revolt – the biggest since 139 Labour MPs voted against the Iraq war in 2003 – Britain will now have a new fleet of Trident nuclear submarines.

During the day, two more parliamentary private secretaries – Stephen Pound and Chris Ruane, aide to the Welsh Secretary and the deputy leadership contender Peter Hain – resigned, bringing to four the number who left government posts over the issue.

But with Conservative support Mr Blair and Mr Brown secured comfortable Commons majorities for renewing the existing system by developing three or four new submarines to replace the Vanguard-class, which will start going out of service in 2022. It means the country will have a nuclear deterrent for at least another 40 years and that Mr Blair has helped Mr Brown to remove one of the most difficult issues that could face a Labour leader.

In the final day of persuasion, Mr Blair and other ministers told MPs that although they were voting for the principle of a nuclear deterrent, there would be further votes during future Parliaments. Margaret Beckett, the Foreign Secretary, and Des Browne, the Defence Secretary, moved to placate MPs such as the former minister John Denham, who had been calling for final decisions to be deferred.

In a letter, the ministers emphasised that the decision to replace Trident would not stop a future Parliament from looking again at the issue. “Further decisions will be required on the precise design of the submarines and whether we need four or three to maintain the deterrent,” they wrote.

“The White Paper also notes that we will need to decide whether to renew or replace the warhead, whether to participate in any US programme to develop a successor to the D5 missile and, subsequently, whether to acquire such a successor.”

The move appeared to have some impact, as did the unusual decision of the Government to allow some parliamentary aides unhappy about the decision to miss the vote. Mr Browne was called to order by the Speaker as he accused two of his Labour colleagues of “dishonesty” in their arguments.

He told MPs that they needed to take a decision now to start the process. The Government had deliberately chosen to bring the debate to Parliament at the start, rather than make decisions in secret and present them later as a foregone conclusion.

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