Up to 150 pupils "rampaged" through the corridors of a new academy last week as a pupil protest degenerated into vandalism.
In widespread problems at Oasis Academy Mayfield, in Southampton, staff are also threatening to ballot for industrial action unless urgent changes are made to the way the school is organised.
The school, which only opened last month, is sponsored by Oasis, a Christian charity and major academy sponsor. It already runs nine schools and is having talks about opening a further three.
But in a major blow to the credibility of the academies programme, John Denham, the local Southampton MP and the Universities Secretary, has questioned whether the sponsor has the experience to run the school. Pete Sopowski, the NUT's area representative, said the school's management had been "arrogant" in refusing to listen to the views of other people.
Ron Clooney, the NASUWT representative, said: "The school is a disaster. Parents, pupils and staff are unhappy with the way it's being run. The spirit and caring ethos of the school has had a kick in the guts. Its heart has been torn out. Considering its being run by a Christian organisation, it beggars belief the way they are dealing with the teachers and the kids.
"The protest by the Year 11s was hijacked by pupils who went on the rampage. They should not have done it, but they are upset."
The academy was created from the merger of Woolston and Grove Park schools.
Pupils are understood to be unhappy that promised improvements to the curriculum have not been delivered. They also complained the split-site arrangement means that teachers do not have enough time to speak with them.
Staff claim that because they are being bussed from one site to another they are losing contact with pupils and are also having to give up their lunch breaks to travel.
"Staff have lost ownership of the corridors because they are too busy rushing to get the bus from one site to another," said Mr Sopowski. "This shows that schools should be run by local authorities, not well-meaning amateur organisations."
Teaching unions have now given the school a deadline of November 3, the first day after half-term, to agree timetable changes or they will seek a ballot on industrial action.
Ruth Johnson, the school's principal, said the pupil incident was very serious but had been exaggerated. She said around 40 students had been involved. Five were permanently excluded from the school as a result and another 25 were given temporary exclusions.
One of those permanently excluded was a boy who is alleged to have threatened a teacher with a small knife being used in science.
"I wrote to all parents to tell them that there had been a serious incident and to explain what happened," said Mrs Johnson.
"It is the sort of thing that sadly does happen from time to time. It was boisterous, totally inappropriate and very serious. But it was brought under control quickly.
"Pupils have naively been saying that they want their old school back, but that can't happen. Maybe the decision to close the schools was not handled as well as it could have been. We need to move forward."
Steve Chalke, the founder of Oasis, visited the school the day after the pupil protest to tell them that the behaviour had been unacceptable. But Mr Denham has cast doubt on the ability of Oasis to make successful progress.
Speaking to the Southampton Echo, Mr Denham said: "This is only the second year it's responsible for any schools anywhere in the country. They may need to look at how they can get in some more expertise in to strengthen, not the headteacher, who I know well and was a successful headteacher elsewhere in the city, but the governance of the school."
Christine Blower, the general secretary of the NUT, said: "It is amazing that the secretary of state of a major education department has said an academy sponsor needs help because it is so inexperienced.
"What problems are academies supposed to solve? The solution has become the problem."
Oasis was chosen to run two academies in Southampton over a consortium of local colleges, universities and businesses, even though the council's own assessment found that the consortium was more likely to raise standards.
A survey of local parents also favoured the consortium.
Mr Denham said at the time that the Conservative council had "snubbed" the city's biggest employers and ignored its officers.