The Cambridge-educated head has held the position since 1986. The school was ranked 51st in the performance league tables for independent school A-level results last week.
Bob Alexander, clerk to the college governors, confirmed that an internal inquiry is taking place. Christopher Field, the deputy college master, has been appointed acting head.
Mr Alexander said: "We hope this will be cleared up as quickly as possible. It will involve further meetings with the governors and could take up to half a term to be resolved."
Police are not involved in the inquiry.