THE Minister for Health Sussan Ley has hit back against claims the Federal Government axed funding to the Healthy Kids Check under the new budget.

Funding to the comprehensive health check for children aged three to five, introduced by Labor in 2008, will cease in November to save about $144 million over four years

But Ms Ley assured parents can still access a pre-school health check for their child at their local GP, funded through Medicare.

"I want to reassure parents that they can still access essential, Medicare-funded pre-school health checks for their children through their local GP or through a state nurse-run service," she said.

"I also encourage parents to do so due to the important early intervention Australia's highly-skilled GPs and nurses can provide our children."

Dr Ross Hetherington at Condamine Medical Centre said, while he is unsure how the changes would affect local services, continued funding would be beneficial.

"If the funding is to continue I'd certainly be very happy about that," he said.

Clinical Services Manager of BUSHkids, an organisation providing primary health care to children in rural Queensland communities, Susan Harrison said early check-ups are important.

"Identifying children for early intervention is important for having good health outcomes," she said.

"We can make the biggest changes to a child's health when we identify a problem early."

Ms Ley said the current service duplicates similar state government-run health programs for children.

A Darling Downs Hospital and Health Service spokesperson said the Warwick Hospital's Child and Family Health Clinic in Percy St provides children's health checks.

"These checks are carried out by trained child health nurses who can assess a child's height, weight, eye-sight, hearing and other general developmental milestones," they said.

Ms Ley said savings would be redirected to "other health policy priorities".

She also said there would be no restrictions placed on how long a visit can take, as is the case now, and the only change is the Medicare items GPs can bill to those accessing the check.

An hour-long check, for example, is said to currently cost $268.80, while the same check delivered through a standard GP visit would cost $105.55.

"Instead of GPs billing a special Medicare item worth hundreds of dollars per visit, they will instead be able to deliver the pre-school health check through a standard GP item worth about half that," Ms Ley said.

"This is a sensible decision considering the annual cost of delivering pre-school health checks through current billing practices has skyrocketed 1000 per cent in seven years, despite take up of the checks by parents increasing at just a third of this rate."