The NASUWT, Association of Teachers and Lecturers and Association of School and College Leaders backed the Government in turning down heads' request for a review of the half-a-day a week given to teachers for marking and lesson preparation (PPA).
This comes at a sensitive time for the social partnership - the mechanism under which the unions plus the Professional Association of Teachers, employers and support staff unions get privileged access to ministers and officials.
Ministers and special advisers are questioning the value of arrangements which exclude the bigger heads' organisation and the National Union of Teachers. But key civil servants remain committed to them.
Mick Brookes, NAHT general secretary, said heads in areas which receive below-average funding were finding it difficult to provide teachers with their legal right to PPA time.
But his demands were rejected at a meeting at the Department for Education and Skills earlier this month. He was told the NAHT could not set preconditions if it wanted to rejoin the partnership.
The union was forced to quit the social partnership in March 2005, two years after signing the workforce agreement, because of a membership revolt over funding. Mr Brookes, a former president and head of a Nottingham primary school, was among those who wanted to pull out.
At the Trades Union Congress last week, the NASUWT won the TUC's backing for a motion calling for the jailing of employers who fail to comply with teachers' statutory rights. Chris Keates, the union's general secretary, said: "Flagrant breaches of the law take place every day in schools and other workplaces across the country."
Mr Brookes said he was hopeful the NAHT would eventually rejoin the social partnership.