Despite opposition from the leadership, representatives of Natfhe, voting before the merger, voted 106 to 57 against the pensions deal.
The motion said it was "morally and politically unacceptable" that those joining the profession in the future would get a worse deal than those who were already in the scheme.
Paul Russell, from the Yorkshire and Humberside region, said: "We have had a defeat. But we don't have to accept this is the end of the line. Let's say it's not good enough and we're going to start doing something about it."
Mick Barr, vice-president of the national executive committee, opposed the motion, saying that any action was unlikely to succeed now that the other unions had accepted the deal.
"Last year, there was momentum," he said. "We had a united front. The Government was forced into a partial retreat because the public sector unions worked together."
He said that, despite its weaknesses, the agreement also provided benefits for which Natfhe had been campaigning for years, such as benefits for unmarried partners and automatic membership for part-time workers.
The motion was part of a series condemning the pensions deal. Delegates said it was "propaganda" that there was a financial crisis which meant pensions were unaffordable. Mark Campbell, from the London region, said:
"We cannot and should not be selling out future workers, particularly in education. The people who will be suffering are going through teacher training now. We have got to defend these workers.
"The whole so-called pensions crisis is because we haven't got enough money - but we've just spent pound;5 billion on bombing Iraq. Employers are paying less tax now than under Margaret Thatcher. Tax the rich, fund our pensions and stop the war. That's what we should be doing.
"We shouldn't be on our knees, begging for crumbs."