Fees for under 13s range from $10 to $18 at Windsor Medical Centre to $49 at Ponsonby Medical Centre.
Anna Young, general manager at Francis Street Medical, said the decision not to join the scheme was driven by capacity issues, rather than financial considerations.
Marlborough has a shortage of GPs, Young said, with waiting lists to enrol.
"We have eschewed this 'popular' move to ensure we can continue to offer a good level of service to all our patients at a time of winter illnesses and a recognised doctor shortage."
Young said the upfront money given to practices that joined the scheme equated to about two visits by an under 13 per year, and the zero fees scheme for children under 6 had increased workloads.
"Notably, GP appointments can be utilised to achieve free medication where a doctor's input is not required."
The Francis Street team's decision not to join the scheme was also influenced by the local hospital starting a project to shift 5000 "unnecessary or inappropriate attendances" at the emergency department to primary care.
"We feel that the scheme was politically motivated but inflexible and ill-thought-through. We continue to review the position," Young said.
Other GPs could not be reached for comment.
Health Minister Dr Jonathan Coleman last month cited data that showed that in the 12 months since the zero-fees policy was introduced, children under 13 had visited their enrolled GP 17 per cent more.
The number of prescriptions dispensed increased by 24 per cent over the same period.
New Zealand First health spokeswoman Barbara Stewart has called for GP visits to be free for children, even if they are not enrolled at the practice. That "hole" in the policy meant some families were waiting until after 6pm to visit an after-hours surgery or hospital emergency department to get a free assessment, Stewart said.
General practices not providing zero fees for enrolled children under 13
• CityMed Doctors, Auckland central
• Epsom Medical Centre
• Ponsonby Medical Centre
• Windsor Medical Centre, Albany
• East Coast Bays Doctors
• Francis Street Medical*, Blenheim
• Torbay Community Doctor*
* Do provide free visits for 0-5-year-olds.
Source: Ministry of Health/practice websites