Nick Clegg faced the first crisis of his brief leadership of the Liberal Democrats last night as the Government comfortably saw off demands for a referendum on the Lisbon treaty.

Three of Mr Clegg’s senior spokesmen quit in order to vote for a referendum. Ten other Lib Dem MPs rebelled, some of them junior members of the front bench.

As Gordon Brown defeated the all-party calls by 63 votes, Mr Clegg accepted the resignations of David Heath, Alistair Carmichael and Tim Farron, because they were not prepared to follow his orders to abstain.

The reverse is bound to overshadow the party’s spring conference in Liverpool this weekend, Mr Clegg’s first important party event since he became leader in December.

Allies of Mr Clegg said that the decision to hold firm and insist on abstaining on the votes for a referendum showed that he had firm principles and leadership. They say that Mr Clegg, as leader, has to insist on collective responsibility in his front bench team and failure to take action would have looked weak. “With the in-out vote, we have a clear position to take us into the next election, unlike the Tories,” said one ally.

Privately many MPs, including those supporting Mr Clegg’s position, wondered why he was picking a fight on the issue when he could have allowed the party a free vote.

By ordering his MPs to abstain he got the worst of both worlds: criticism for apparently weak leadership but a revolt all the same.

MPs complained that if he had allowed a free vote his MPs from Euro-sceptic constituencies could have opted for a referendum and avoided local criticism, while the majority would still have opposed a referendum and helped the Government to get its way.

Last night Mr Clegg sought to play down the revolt, insisting that he had the support of the “overwhelming majority” of the parliamentary party.

“These things happen on issues with the importance of Europe,” he told Channel 4 News. “It is not such a big thing that from time to time in a parliamentary party there is a division of opinion.”

He said that he would be speaking to a number of junior spokesmen who joined the revolt in the coming “hours and days” but appeared to rule out further sackings.

“Do I reassert my authority by having some great cull? This is not the way that politics works. I will make sure – have made sure – that there is discipline in the overwhelming majority of the parliamentary party,” he said.

According to one Lib Dem MP the rebellion was sealed after unsuccessful meetings at Mr Clegg’s Commons office when the trio opted to resign rather than be sacked. Even the three frontbenchers told Mr Clegg that they believed he should sack them.

Lib Dem sources insisted last night that the process had been “amicable” and came after lengthy discussions that established the party’s position.

Mr Clegg only insisted on resignations from members of his shadow ministerial team. Other frontbenchers faced a rap from the whips.

All three senior spokesmen are likely to return to the front bench after an interval. For now, Chris Huhne, the home affairs spokesman, will take on justice, Steve Webb’s environment team will take on the countryside brief and Michael Moore, the international development spokesman, will take on Scotland and Northern Ireland.

Mr Clegg said: “I am grateful for their offer of strong support from the back benches, and I know that they will all play a very significant role in the future of our party. I’m not banishing people to outer Siberia.”

Earlier in the Commons, Mr Clegg, who became leader after the short reign of Sir Menzies Campbell, was mocked by all sides. Michael Ancram, a former Tory minister, said: “This debate is going to be remembered most for the impressive sight of the Liberal Democrat Party marching, with sound and fury, courageously towards the fence upon which they have been ordered to perch.”

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