Sunderland's Grindon Hall Christian School and Durham Free School were both rated inadequate following inspections in November.
The schools subsequently complained about the conduct of the inspectors.
Ofsted said no issues were raised during the inspections. A full investigation is under way.
Grindon Hall principal Chris Gray said the inspector's questioning was "hostile" and "inappropriate", claiming pupils were asked leading questions about homosexuality, race and other faiths.
In a statement, Ofsted said initial interviews with the three inspectors who visited the schools had found no evidence they acted incorrectly.
The statement said the allegations were serious but had not been raised with inspectors during the visits.
Ofsted said: "We have undertaken a detailed examination of the evidence base, interviewed each of the three inspectors who carried out the inspection and have held a separate meeting between the principal and Ofsted's North East regional director in respect of these allegations.
"To date, we have found no evidence to indicate that inspectors failed to act with care and sensitivity and to ask age-appropriate questions when they spoke to pupils, as they are trained to do."
Durham Free School complained the inspectors based their conclusion that "pupils were not being prepared for modern British life" on an interview with one student.
Ofsted said: "In reaching their conclusions about the effectiveness of the school's work inspectors considered a wide range of evidence.
"Discussions with students formed just a part of the evidence."
Ofsted criticised both schools for not tackling "prejudice-based bullying" and the use of racist or homophobic language by students.
Both schools said they did not recognise Ofsted's portrayal of them.
The body also said it visited two other schools in the North East in November but neither raised any concerns.
After their report was published, education secretary Nicky Morgan said she was terminating the funding for Durham Free School, which has 94 pupils.
Ofsted says it found no evidence its inspectors acted inappropriately while visiting two free schools subsequently placed in special measures.