Plans for a new school federation backed by London University's Institute of Education are facing severe delays following teacher walkouts in protest at the scheme.
NUT members striking to prevent a community secondary from becoming a trust say they fear for the school's future if its leaders are given more powers.
The opposition means that final arrangements have stalled.
This is the latest in a spate of industrial action at Norlington School for Boys in Leyton, east London. Governors have already survived two no-confidence votes by staff.
Former headteacher Jennifer Bax resigned after an earlier strike in the summer.
Teachers' leaders said their members are against Norlington becoming a trust school because they do not want to be employed by governors instead of the local authority.
Another local secondary will be involved in the Leyton Learning and Leisure Trust, which was scheduled to be in place by September 1. Institute of Education (IoE) staff were due to act as governors or trustees.
But the University and College Union, which represents academics, has joined the NUT in opposing the plans, saying it is "inappropriate" for the IoE to become involved in trusts.
Norlington was closed this week during the two-day walkout, organised by the NUT. Despite efforts by conciliation service Acas to resolve the dispute, half the 52-teacher workforce picketed the school on Tuesday and Wednesday.
NUT organisers said problems at Norlington have been resolved in the past only after intervention by local authority mediators. Teachers fear disputes will escalate if the school is taken out of its control.
They claim that governors have failed to "show faith" in Norlington and have done little to promote the 600-pupil school in the local community - especially among Muslim parents who would favour the single-sex education offered by Norlington.
"The idea that this governing body could be the actual employer of teachers - that it would be running the school independently of the authority - is a frightening prospect," said Rinaldo Frezzato, Waltham Forest NUT secretary.
"The commitment of staff governors to the school stands in strong contrast to other governors. Teachers really believe in the school - I've rarely come across such a cohesive team. But the governors are not doing anything to build Norlington up. We don't want to close the school, but this is the only way to save it."
Interim headteacher Ruth Woodward took over after Ms Bax's resignation, which came after a two-day strike in July over proposals to move the school to trust status.
Staff at the school were among the first in the country to strike over flexible working in support of a teacher who was refused a job-share after maternity leave.
Lee Boyce, head of English, wanted to return to her post on a three-day week job-share. The school offered a compromise of part-time working for four days a week.
Councillor Liaquat Ali, cabinet member for children and young people at Waltham Forest Council, said: "I am extremely concerned that the welfare and education of Norlington pupils continues to be threatened by a dispute that is completely out of their hands.
"This dispute relates to a decision taken by the school's governing body, which they believe will best benefit the entire school and its pupils. As such, the council fully supports the governing body's decision."
An IoE spokesman said discussions about the trust were "at an advanced stage but were not finalised".