A full review of the patient notes of Dr Nic Driver is now being launched by the Royal Surrey County Hospital in Guildford, where he works.
The review will look at notes going back to 2002.
It is understood that concerns were raised by a fellow healthcare professional.
The General Medical Council (GMC) has been informed of the review but is not involved in carrying it out.
A spokeswoman for the Epilepsy Society said: “Clearly, it would be wholly inappropriate for us to comment on this specific case as we are not fully informed of the facts.
“However, if your child is currently receiving treatment for epilepsy, it is important that you do not alter or stop their anti-epileptic medication.”
No children have died as a result of the treatment given by Dr Driver, according to the hospital.
A letter has been sent to all patients involved advising them of the situation concerning the “medical practice” of Dr Driver.
The review concerns 569 patients who have been seen with epilepsy or a related disorder since Dr Driver’s appointment to the trust in 2002.
Hospital officials stressed that Dr Driver had previously seen many other children in general practice but the inquiry only relates to youngsters he saw with epilepsy.