It came as the Speaker of the Commons, Betty Boothroyd, ordered an investigation into angry claims that the Government may have "doctored" the Prime Minister's assurances to MPs in Hansard, the Commons official report, to cover up for a breach of faith over the linkage of prisoner releases with the decommissioning of weapons.
Andrew MacKay, the Tory Northern Ireland spokesman, said he could not sign a "blank cheque" for the Government, but he denied he was breaking the bi-partisanship Labour maintained in Opposition.
However, last night's vote caused a deep rift in relation, which could break down 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 William Hague to get a grip on his Northern Ireland spokesman.
Tory sources said Mr Hague had fully endorsed the line taken by Mr MacKay at Wednesday night's Cabinet. 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."
The row centres on the assurances given in the Commons on 6 May by Mr Blair. In the transcript of the exchanges with Mr Hague, Mr Blair 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 was omitted. Mr MacKay said the report had been "doctored", but that charge was denied by the Prime Minister's official spokesman, who said Number 10 did not routinely check Hansard for the accuracy of its reports of Prime Minister's questions.
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, as he was campaigning in Ulster for next week's elections to the new Northern Ireland Assembly.
The Tories claimed 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.
Mr Trimble secured a late concession from Mo Mowlam, the Northern Ireland Secretary, to require the Commission to implement the terms of the peace agreement, specifically involving decommissioning.