The program, which starts on July 1, will be predominantly managed by GPs who will refer children with troubling behaviour to psychologists or paediatricians.
Mr Butler admits there is always the danger of misdiagnosis or oversubscribing and says that's why child care experts have been spending months getting the program "precisely right".
"Parents can be confident that when they go to a GP or a practice nurse in a GP surgery to check that just before their child starts pre-school or steps into primary school, that they're developing in a way that we all hope and expect that they will be," Mr Butler told journalists in Adelaide.
He said the program was aimed at picking up problems early so they can be dealt with and allow the child to enter preschool and primary school in the best position possible.
He said this $11 million program is the latest addition to the government's $2.2 billion mental health reform package where children are checked for heart, eyesight and other physical health issues.
The mental health check itself will be mostly done by GPs under the Medicare system.
"The experts who have been designing this tool have made it very clear that their overriding objective has been to do no harm ... to provide a positive opportunity to families to take their children at that critical time of three years of age," Mr Butler said.
"Obviously, we need to make sure through the advice of the clinical experts that it's conducted in the best way possible and that there's not an overreaction.
"I'm very confident that the people we have around the table designing this piece of work have that absolutely at the front of their mind."
The government experts more than 27,000 children will benefit from additional support after being tested.
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