The B4 School check, due to start in September, is designed to identify health, behavioural, social and developmental issues which could affect a child's ability to learn.
Included are a general health questionnaire, hearing and vision tests, height and weight measurement, and questionnaires for parents and early-childhood teachers about the child's behaviour and development.
The Otago and Southland District Health Boards are working together to deliver the programme.
Regional planning and funding officer Chris Fraser has repeatedly warned the boards not to underestimate the size of the project.
"Just setting up the infrastructure and getting the thing up and running is substantial. There are literally hundreds of schools spread out all over the district."
The checks will not be compulsory and decisions are yet to be made on who will be responsible for providing the checks in the South.
Balclutha GP Branko Sijnja said many practices already offered free pre-school health checks, but the new checks appeared to be more elaborate.
"It ties together the sort of thing public health nurses have been doing and puts it all together in one check.
I think it is worthy of support," Dr Sijnja said.
The B4 School check is being extended across the country and has been trialled by Counties Manukau and Whanganui District Health Boards.
It is estimated to cost $23.6 million over four years.
