The vote came after the Speaker of the Commons, Betty Boothroyd, ordered an investigation into angry claims that the Government may have "doctored" a report in Hansard to cover up for a breach of faith over the linkage of prisoner releases with the decommissioning of weapons.
The row centres on the assurances given to MPs in the Commons on 6 May by Tony Blair.
In the transcript of the exchanges with Mr Hague, the Prime Minister explicitly agreed with the Tory leader that prisoners "should not be released early until the organisations to which they belong have substantially decommissioned their weapons".
But in the official report, that exchange had been omitted.
Andrew Mackay, the Conservative's Northern Ireland spokesman, said the report had been "doctored", but that charge was denied by the Prime Minister's official spokesman, who said No 10 did not routinely check Hansard for the accuracy of its reports of Prime Minister's questions.
When the vote came, the Tory opposition was not universal. Douglas Hogg, the former agriculture minister and Tory MP for Sleaford and North Hykeham, defied the rest of his party and voted with the Government in favour of the agreement.
Many senior Tory figures, including the party leader William Hague, did not vote.
Others who were in the House, including John Major and his former Northern Ireland secretary Sir Brian Mawhinney, also decided against voting.
Mr Mackay, said he could not sign a "blank cheque" for the Government, but he denied he was breaking the bipartisanship that Labour had maintained while in opposition.
However, last night's vote caused a deep rift in relations, which could break down completely if the Tory peers carry out the threat to reject the Bill in the Lords.
Downing Street officials angrily said Labour had never broken the Northern Ireland deal with the past Tory government and questioned whether there was "clear thinking" in the Tory leadership.
That was seen as a challenge to Mr Hague to get a grip on his Northern Ireland spokesman following claims that he was running out of Mr Hague's control.
Tory sources said that Mr Hague had fully endorsed the line taken by Mr Mackay at the Shadow Cabinet on Wednesday night.
Mr Mackay said: "We will support the Government wherever we can when they are right, but as an Opposition we will oppose them when they are wrong.
"We don't like the idea of early prisoner releases. We reluctantly accepted that as part of the package and we will hold our noses and support the Government, but we are not prepared to see the Government mislead the people of Northern Ireland on the promises they have made," he added.
The Tories faced further criticism that they were taking a harder line against the third reading of the Bill than David Trimble, the Ulster Unionist leader.
He was not present for last night's vote. None of his party's MP's supported the Bill.
The Conservatives claimed that the Secretary of State was not required by the legislation - despite promises during the referendum campaign - to ensure that weapons decommissioning was going on before prisoners were given early release.
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