The Government scraped home by only nine votes as Ministers were accused of "buying" votes in order to win amid claims of deals to woo the Democratic Unionist Party (DUP) and wavering backbenchers.

Days of personal calls from Mr Brown and senior Cabinet Ministers, a raft of safeguards limiting the measures and a shopping list of concessions finally brought enough Labour MPs on board but still left 36 rebelling in the biggest revolt since he moved into Number 10.

But while Downing Street may breathe a sigh of relief, the battle is far from over as Mr Brown now faces the prospect of the Bill being rejected by the House of Lords where former Cabinet ministers Lord Goldsmith and Lord Falconer have already expressed their opposition.

Last night both the DUP and Downing Street denied any deal had been struck to guarantee the nine unionist votes, but Labour rebels claimed the DUP had obtained guarantees on abortion and keeping revenue from water rates in Northern Ireland.

It also emerged Mr Brown met MPs last week to discuss a massive compensation scheme for victims of "miner's knee", although any link with the 42 days vote was denied. There there was also speculation that the Government will back the easing of sanctions on Cuba to appease Left-wingers.

Shadow Home Secretary David Davis said: "We won the argument, the Government bought the votes. Ministers utterly failed to provide the evidence in favour of 42 days in the Commons, and the measure is likely to be rejected in the House of Lords.

"Amidst widespread reports of vote-buying, the Government did not have the Labour support to win – leaving its Parliamentary authority in tatters."

Liberal Democrat leader Nick Clegg said: "What we've seen in the House of Commons is the sacrifice of principle in order to save the skin of a sinking Prime Minister."

Three Yorkshire MPs – Selby's John Grogan, Halifax's Linda Riordan and Batley and Spen's Mike Wood – were among the Labour rebels at the end of a dramatic day in Westminster.

After weeks of negotiation and debate over the Counter-Terrorism Bill, Mr Brown and Tory leader David Cameron clashed at Prime Minister's Questions before an afternoon of debate in the Commons.

The Bill would allow police to detain terrorist suspects without charge for up to 42 days on one-off occasions where there was a severe terrorist threat. The current limit is 28 days. Concessions offered to backbenchers mean the Commons will have to vote to approve a decision to let police go beyond 28 days, and there was a last-minute promise of compensation for innocent people who are held.

But Mr Cameron said: "Isn't it clear that terrorists want to destroy our freedom and when we trash our liberties, we do their work for them? This is not about the future of our Prime Minister. This is about our liberties."

Mr Brown, however, said the first duty was protecting national security. "We fail in our duty if we do not take preventative measures," he said.

"I say in sorrow rather than anger, it is no use opposition for opposition's sake. We have to take no risks with security."

Throughout the day Labour whips continued to pressure wavering MPs.

Labour rebels claimed the DUP had convinced the Government to block efforts to use the Human Embryology and Fertility Bill, currently going through Parliament, to loosen abortion rules in Northern Ireland, while Tory MPs claimed deals worth £1.2bn for the province had been agreed. The DUP and Downing Street denied any deal was done.

In the build-up to the vote, Left-wingers called for Britain to distance itself from American foreign policy, such as opposing sanctions against Cuba. Downing Street would only say Britain's position on Cuba was "kept under review".

In the end, the nine DUP votes were crucial as the Government won the vote 315 to 306. Tory Ann Widdecombe, Ukip MP Bob Spink and Ulster Unionist Lady Sylvia Hermon also backed Mr Brown.

Mrs Riordan said: "Clearly, this had little to do with justice and everything to do with a Government questioning the motives of people like me and offering deals to all and sundry. Ironically, we must now rely on the unelected Lords to protect our democratic rights."

Mr Grogan said it was the "worst possible result" for Mr Brown, because the issue would now drag on. But Home Office Minister Tony McNulty said it would be "perverse" to interpret the vote as damaging to Mr Brown.

More coverage:
Whips' pressure pays off as 42 days defeat averted>>
A battle won. . . but Brown faces more backbench woes>>