Barbara Matthews, head of maths at Northfleet school, faced the charge at a meeting of England's General Teaching Council's induction appeals committee last week. The allegation was made by Samuel Kisiedu, who failed his induction year at the school in 2003.
The school claimed that Mr Kisiedu, from Ghana, failed his NQT year because of problems with classroom management and pupil assessment.
The committee agreed with the school's assessment, but decided there were weaknesses in its induction process and ruled that Mr Kisiedu should be able to repeat his last two terms at another school.
Mr Kisiedu, who has a son and lives in Croydon, has been unemployed since last July. He did his teaching practice at the school.
He claimed racial discrimination on the grounds that Mrs Matthews had demanded his reports were of a higher standard than those of another teacher.
He said: "There were people who were writing reports in the department not to the standard Mrs Matthews expected and nothing was done, probably because of their colour."
Dr Jill Key, head at Northfleet, said Mr Kisiedu had not been singled out, saying she too had been criticised by Mrs Matthews. "Mrs Matthews has read my reports and returned them to me because my spelling is not what it should be," she said.
Dr Key said the other teacher cited by Mr Kisiedu had been off sick after a heart attack, and had not needed to write the reports in the first instance.
However, she admitted Mr Kisiedu's and Mrs Matthews's relationship had broken down by the beginning of the spring term: "Mrs Matthews got very frustrated that her advice and guidance were being ignored."
Robert Mayhew, Mrs Matthews's deputy, took over as Mr Kisiedu's mentor in the spring term because of the deteriorating relationship.
Even so, Peter Britcliffe, committee chair, said Mr Kisiedu's chances of passing his induction year had been seriously disadvantaged by the breakdown in his relationship with Mrs Matthews, and "lax" monitoring in the autumn term.
Mr Kisiedu's claims that targets had not been set for him and that he had been unable to observe other teachers were not upheld. There was insufficient evidence to support his claim that he had not been allowed to attend professional development courses.
Speaking after the hearing Mr Kisiedu said: "This gives me the opportunity to carry on teaching. The number of years I've invested in teaching haven't become useless."