Steve Davies told AMs officials were "concerned" about the volume of early entry.
It follows criticism from Education Secretary Kirsty Williams that children were being "banked" at lower qualifications.
Mr Davies said the government wants to take action on the issue in the autumn.
Ms Williams expressed concerns earlier in May that the focus on raising GCSE attainment to C grade has led to "unintended consequences", with some children put in for early entry to bank a lower qualification instead of potentially reaching higher.
The senior civil servant - asked about the issue of "early entry as a way of gaming the system" by Labour AM Lee Waters - said the Welsh Government advice was that decisions around early entry were made "in the interests of an individual child".
He told the assembly's public accounts committee that this year that some schools have conducted early entry "almost to test the system".
But he added: "I do believe... there are also those out there who are gaming."
Mr Davies acknowledged: "Sometimes that's the pressure that the system we have puts on them.
"I'm not in any way justifying it, but I can understand that people will resort to that."
Mr Davies said the government was working with Qualifications Wales (QW) to identify "the scale of the problem" with a report from the body due in September.
He added Ms Williams is "very aware of it" adding that action will be taken in the "early part of the autumn term" following the review.
Some schools are "gaming" the exam system by entering children early, the Welsh Government director of education has said.