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

Despite last-minute concessions and a massive persuasion effort by the whips 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 again, voting directly against a motion to update the Trident system.

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 support 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 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 any Labour leader.

The revolt would have been larger but for a final day of persuasion led by Mr Blair. He and other ministers told MPs that although tonight they were voting for the principle of a nuclear deterrent there would be further votes at different stages during future Parliaments.

In a late move, Margaret Beckett, the Foreign Secretary, and Des Browne, Defence Secretary, moved to satisfy MPs such as the former minister John Denham, who had been calling for final decisions to be taken in a later Parliament.

In the letter the ministers stressed 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.

“It will fall to future Governments and Parliaments to discuss the most appropriate form of parliamentary scrutiny for these downstream decisions.”

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 wound up the debate by accusing two of his Labour MP colleagues of “dishonesty” in their arguments.

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

Mr Ruane’s resignation letter said: “I believe the Government’s proposals on Trident, at this stage, would work against the long-term goal of reduction in nuclear capability.

“I could therefore not support the resolution.”

Nigel Griffiths, who resigned as deputy Commons leader over the issue on Monday, said Britain must lead by example in global efforts to end the nuclear threat.

“The world is watching us now. Let us be leaders for peace,” he said.

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