The Duke Of York's Royal Military School, near Dover, is an academy with military traditions.
According to Ofsted, in September 2012 there were two "serious welfare incidents" and in May 2011 a "serious bullying incident".
Head teacher Chris Russell said issues in the report had been "dealt with".
The school, which dates back to 1801, was formerly funded by the Ministry of Defence for pupils whose parents were or had served in the armed forces.
In September 2010 it became an academy and open to pupils of all backgrounds.
Mr Russell said: "A lot of the Ofsted report was based on historical issues which have now been dealt with and the school is moving very rapidly forward and there has been major cultural change."
He said neither of the 2012 incidents were to do with bullying and that 16 staff members left in 2011 because of the change to academy status.
A new leadership team took over in summer 2012.
"I think there is a huge change from the independent sector to the state sector and that increased forensic accountably," he said.
"A number of staff found that very difficult and for their own particular reasons decided to go."
The Ofsted report said following the "serious bullying incident" in May 2011 an internal inquiry was undertaken by the governing body.
The report added: "The senior leadership team understands its own strengths and weaknesses and there are preliminary indications that the current leadership is improving the welfare provision at the school.
"There are clear development plans which are being implemented but there is still some way to go to ensure these are fully implemented or embedded."
A military boarding school has been subject to an emergency inspection by Ofsted over concerns about pupil welfare.