The Civil Public and Services Union, which represents lower paid civil servants, has voted to accept the Haddington Road Agreement on public sector pay and conditions.
However, General Secretary Eoin Ronayne accused the Government of putting a gun to members' heads by passing emergency legislation to permit harsh cuts in pay and conditions.
He said members had been left with "Hobson's Choice" over the deal.
The CPSU had walked out of talks on the Croke Park II proposals, and had spearheaded opposition to the deal, which involves longer working hours as well as cuts in earnings for public servants.
Despite the CPSU executive recommending rejection of the HRA, members voted by 54.6% to 45.3% to accept the latest proposals.
The turnout was 64%.
The union had rejected the Croke Park II proposals by a margin of 86%, with a turnout of 82%.
Mr Ronayne said the result could not be seen as an endorsement of Haddington Road, but rather as a result forced by Government through what he called intimidation and fear.
He said the passing of emergency legislation, with what he called draconian ministerial powers to change the conditions of Government employees, had left members with a gun to their heads.
The CPSU executive will meet tomorrow to consider how to campaign against politicians who had voted for the Financial Emergency Measures in the Public Interest emergency legislation.
Meanwhile, plasterers' union OPATSI has voted to accept Haddington Road with 75% of members in favour.
The Irish Medical Organisation has also voted to accept the deal, with 67% of its members voting in favour.
So far the Unite trade union is the only union to formally reject the deal in a ballot.