More than 800 claims are being made against staff, according to the NASUWT union.
Many of the allegations follow attempts by teachers to discipline pupils who misbehave in class, it was claimed.
The union argued that teachers were seen as "guilty until proven innocent" and can face suspension, police investigations or disciplinary procedures if they are confronted with abuse allegations or claims they used excessive force against a pupil.
Even if a teacher is later cleared, the complaint is still held on record, they said.
Chris Keates, NASUWT general secretary, said the majority of allegations were unfounded and told the BBC that the situation was a "blight" on the teaching profession.
She said: "Whatever the outcome of the investigation, that will be on the teacher's file. If that teacher applies for another job that allegation will be resurrected under the Criminal Records Bureau check.
"So you could say that every one of those 800 teachers has got a blight over their career for the rest of their time teaching."
While no-one doubts that children needed protection, Miss Keates added: "This presumption of guilt is one of the major flaws in the current system."
Ministers said they were looking at the guidance on accusations against teachers.
A spokesman for the Department for Children, Schools and Families said: "Guidance on more consistent and swifter handling of allegations was issued for education in 2005.
"We are also looking at whether guidance should be amended to make clear that accusations which have been demonstrated to be untrue do not need to be included in teachers' references." Last Updated: 5:57PM GMT 03 Mar 2009