The Charity Commission is investigating allegations of misuse of funds at Gad's Hill private school in Higham.
It has written to the charity-run school's trustees following claims made by former chairman of governors, John Melville, who resigned earlier this year.
The allegations, highlighted in a BBC report, include claims headteacher David Craggs had awarded himself hefty annual pay rises - from a salary of just over £35,000 in 2000 to nearly £169,000 by 2011.
David Craggs Head Master of Gads Hill
It also alleged the headteacher misused school funds - which was at the centre of an internal inquiry by the school in 2012.
However, the Charity Commission was not informed of the school's review, which found Mr Craggs should not be disciplined.
Now it is going to carry out further investigations into the alleged misappropriation of funds.
A statement issued by the commission this morning, said: "The issues brought to our attention (by the BBC) in connection with Gad's Hill appear to require further regulatory assessment and we have written to the trustees asking for their comments.
"While the trustees had informed us of the financial review they undertook, we did not receive any notification of alleged misappropriation of funds.
"Any such concerns are serious, and it is the trustees' responsibility to report these to us in a Serious Incident Report.
Gad's Hill School, Higham
"It is also essential that trustees properly manage their affairs of the charity in accordance with the governing document, including managing conflicts of interest and ensuring that decisions are taken by the appropriate persons.
We await the trustees' response after which we will consider what action, if any, may be appropriate.
Kirsty Hillocks, for Gad's Hill, confirmed the school had received correspondence from the Charity Commission and would be fully co-operating with its requests.
The acting chair of governors said allegations were raised two years ago by a former employee and John Melville, who was chairman of the governors at the time, believed they should be "thoroughly scrutinised".
In a statement released today, Mrs Hillocks said: "At his request, the governing body initiated an investigation, which concluded that the headmaster had not breached any school policy or procedure and therefore would not be subjected to any disciplinary process.
"While the trustees had informed us of the financial review they undertook, we did not receive any notification of alleged misappropriation of funds" - Charity Commission
"In his capacity as chair of the board of governors, John Melville referred a number of these matters to the Charity Commission for its consideration.
"It concluded that the school may need to review some of its internal procedures, but that it had acted appropriately and saw no need for any further action.
"As chair, Mr Melville was fully aware of the course of the investigations and the outcomes, remaining in post until his resignation in spring 2014.
"The headmaster has a very clear view of the direction he wants to take the school, relentlessly striving for school growth and improvement.
"He deservedly has the full confidence of school staff and the governing body."
Police have confirmed they are not investigating Mr Craggs, who is a serving special constable.