Parents at Matravers School in Westbury, Wiltshire, claimed special needs pupils had been 'hidden away' during an inspection – and their claims were supported by a school governor.
But a spokesman for 1,000-pupil school said the allegations were 'untrue and misinformed'.
The row erupted after parents claimed some pupils, including an autistic 12-year-old, were told to stay at home.
Russell Hawker, a Wiltshire councillor who is also a governor at the school, said a 'very small handful' of disruptive pupils were removed because staff were aiming 'to get a good Ofsted report'.
Martin Gillingham said his dyslexic son Jamie, 15, was taken out of mainstream class and instead placed in a special two-day mechanics lesson.
He said Jamie and three others were told it was to stop them causing 'disruption' in front of the inspectors.
Mr Gillingham, 46, told his local paper: "It would appear the school have tried to hide away any child that poses a possible risk of causing disruption.
"They have said their actions were in the best interests of the children. How can it be in the best interests to have a false Ofsted report? Any Ofsted report now holds no weight."
A mother-of-two said she was told by teachers to keep her 12-year-old autistic son at home during the inspection.
The unnamed 37-year-old, whose son also has ADHD and physical tics, said: "I was shocked. My son needs routine, and they took that routine away from him.
"If he has got a problem his needs should be met. As a parent I feel that for those two days he wasn't included.
"My son asked me why he was kept off school for two days. I didn't know what to say to him."
The row came after the school was graded 'requires improvement' during the last inspection in February 2013 and told to do more to help children with extra needs.
The report also said: "Low attainers, students eligible for pupil premium support and most of those identified as disabled or with special educational needs are not making as much progress as their peers."
Governor Mr Hawker said: "Two types of students have been involved in this, one of which was those who are very autistic children whose parents or carers were contacted by the school because of the Ofsted visit and because of the change in routine they would be kept at the Link Centre [a support unit for special needs children].
"The second group were children who had a history of being disruptive in class, that's my understanding.
"I'm very sure that no staff would try to tell children to stay at home.
"There was a very small handful where some people with a track record of causing disruption were taken out of class because you don't know what they are going to do.
"My belief is the school did what was in the best interest of the whole school and their objective is to get a good Ofsted report."
A spokesman for the school said the governor's comments were 'untrue and misinformed'. He said: "The views expressed by the governor were neither authorised or endorsed by the Board of Governors of the school.
"The comments made contain factual inaccuracies.
"Whilst a tiny number of parents of our most vulnerable students were contacted, this was as a supportive and caring measure to alert them that there were some potentially unsettling consequences of the Ofsted visit."
The spokesman added: "Matravers School is proud to be a fully inclusive school that successfully accommodates students with a wide variety of educational needs.
"We encourage parents who have any concerns to contact the school so we can respond to their individual queries sensitively and constructively."
An Ofsted spokesman said: "If inspectors become aware that evidence has not been available or withheld during an inspection, then we would consider whether, had that evidence been available, it would have had an impact on the inspection outcome.
"If so, we could declare the inspection incomplete and return to the school to collect more evidence.
"Deliberately withholding evidence from inspectors would be regarded as a very serious matter."