"There is the potential to increase demand after-hours, and that's a situation that a lot of GPs are struggling with now in terms of the onerousness of after-hours calls," Mr Macara said.
The South was on track to meet the target of 60% of practices signed up to provide the service by July 1, he said.
First practices in the scheme would be concentrated mainly in Dunedin, Invercargill, and Queenstown.
Mr Macara agreed the remaining 40% of practices would be more difficult to negotiate.
"We had a GP tell us in Cromwell ... 'this potentially could be the straw that breaks the camel's back'," Mr Macara said.
Whereas the GP was able to manage getting up once a night for a callout, the new entitlement raised fears this might increase to two a night or more.
It could have a big impact in tourist towns such as Queenstown, where practices could be forced to treat any child, from anywhere in the country.
"We think there's a huge demand that will happen in those tourist areas."
Unlike the under-6s free care expectation on practices during the day, the new entitlement was considered an urgent service practices had to provide.
Some felt they were "dictated to" by the compulsory nature of the new scheme, which was announced before last year's general election.
The Government allocated $19 per child, per year for the entitlement, Mr Macara said.
It was unclear whether this was enough to fully fund the entitlement, he said, which made the negotiating process difficult.
The $28 million policy was paid for using savings from drugs coming off patent, a spokeswoman for Health Minister Tony Ryall told the Otago Daily Times last month.
An update to last week's Southern District Health Board community and public health committee noted 16 of 96 practices in the South still charged under-6s during the working day.
The committee was also advised that progress with the after-hours under-6s entitlement had been slower than expected.
