Tony Mitchell, a national executive member of the Campaign for State Education, questioned the appointment of Dame Suzi Leather, the commission's chair, because her daughter attends a private school.
He also suggested that too many of the commission's board members have links with private schools. Mitchell's letter says he first raised his concerns with the commission in 2005, 18 months before Leather's appointment. "Dame Suzi's appointment seems to be an example of supreme incompetence, at best, by those responsible for preserving legality at the commission," it reads.
A Charity Commission statement said: "It is inevitable in public office that conflicts of interest may sometimes occur, and we take very seriously the issue of declaring and managing conflicts."
It said that educational background should not be a case for withdrawing from discussion, and that last year Leather withdrew from making decisions on this issue because she was paying her daughter's school fees and so had a financial stake in the outcome.
A spokeswoman for the Committee on Standards in Public Life said it did not have the power to look into individual cases.