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.

Sian O'Callaghan, 22, was last seen leaving Suju alone at about 0250 GMT on Saturday to walk half a mile home.
About 400 people took part in the search of Savernake Forest near Marlborough which is due to resume at 1030 GMT on Wednesday.
A £20,000 reward to help find her has been offered by an anonymous donor.
Mobile records put her phone in the area of the 4,500-acre forest 32 minutes after she left the club.
Police say the journey could only have been made by car.
Miss O'Callaghan's friends and her boyfriend Kevin Reape joined the search along with local people, many of whom did not know the missing woman, following a police appeal for help.
Volunteers searching the dense woodland were divided into groups which were then assigned to a specialist police officer.
Mikey Jack, 19, who plays Sunday league football with Mr Reape, said: "A lot of people here don't really know Kevin or Sian but they just want to help any way they can."
Another volunteer, college student Tizanne Gregory, 17, added: "I came here today in the hope of finding Sian.
"I'm just hoping we can do anything to help her parents and it is horrible not knowing where she is."
A police spokesman said Miss O'Callaghan had an LG E900 Optimus mobile phone and asked for anyone who finds one to contact the force.
CCTV footage of Miss O'Callaghan alone in the nightclub has been released in the hope that it will jog revellers' memories.
The black and white footage shows her walking downstairs and outside through the club's entrance, past a small group of men.
A police spokesman said the times shown on the CCTV were about six minutes slow.
He urged anyone who remembered seeing Miss O'Callaghan to contact the force.
Her disappearance has been described as totally out of character.
More than 60 police officers are working on the investigation which is being treated as a missing person inquiry.
Det Supt Steve Fulcher said: "Sian left Suju and walked along the High Street in Old Town and there were a number of vehicles moving through the High Street between 2.55am to 3am.
"We would like to identify the people in those vehicles as possible witnesses.
"I'd also like to hear from anyone who saw any vehicles in or near beauty spots between Swindon and Savernake between 3am and 4am.
"It is very important that people come forward as they may have vital information which will help us to find Sian."
At a news conference on Monday, her boyfriend Kevin Reape, who shared a flat with Miss O'Callaghan, appealed for information to help find her.
A Wiltshire Police spokesman said Mr Reape was not being treated as a suspect in Miss O'Callaghan's disappearance.
Also present at the news conference were Miss O'Callaghan's parents Mick, 51, and Elaine, 48, brother Liam, 24, and sister Lora, 19.
Some schools are "gaming" the exam system by entering children early, the Welsh Government director of education has said.
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Hundreds of volunteers have joined police to search a forest in Wiltshire for a woman who vanished after leaving a nightclub in Swindon.