The Southern Health Board expects to spend $705,935 next financial year on B4 school checks for 3050 children.
In Otago the aim is to reach 1736 children, including 171 considered highly deprived, and 1314 in Southland (181 highly deprived).
Ministry of Health figures show the Otago District Health Board was one of only three boards to reach targets for checks by the start of May.
However, its target involves only 50% of the estimated eligible population of 2031 children.
Each board negotiated target numbers with the ministry, the emphasis being on reaching those children considered to have high needs or from high deprivation areas.
While Otago exceeded its overall target, the figures show that in common with all other areas, it did not reach all children considered to be highly deprived.
Its coverage was slightly more than two-thirds of the estimated number of children in this category.
The scheme's aim is to identify health, behavioural, social and developmental issues in 4-year-olds, which might affect their ability to learn. In Otago by May 6, the board had exceeded its target of 1131 by 44.
A further 45 checks were in progress.
In Southland, where the target was 64% of 1480 children, the ministry figures show that 81.2% of the checks had been completed by early May, but a report to the new Southern District Health Board this week says the Southland results are not accurate because of delays entering the data.
Health Minister Tony Ryall called for a review of the programme last year, after being unhappy with its implementation, but announced in April it would continue.
Some boards were forced to pay back money last year for services not provided.
Mr Ryall said he still has some concerns about the delivery of the programme.
The aim was for 80% of high-needs 4-year-olds to be seen this financial year, but it appeared boards would only see half of that number.
A Ministry of Health audit also found only two in three children referred to specialist services were actually seen by the service.
"The ministry will be requiring DHBs to ensure more high-needs children are checked and more is done to ensure that the children referred on to specialist services are actually followed up," the audit said.
Across the country, the targets range from 15% to 97% of the eligible board populations, and 12 of the 21 boards are aiming for checks of between 50 and 60% of their eligible populations.
Elsewhere, achievement of the agreed targets varied from 4.5% in Counties Manukau, where checks were started later because of a contract delay, to West Coast which had exceeded its target, achieving 104.7%.
South Canterbury was the third board to have reached 100% of its target or higher.
The programme was allocated $9.9 million in the Budget in 2008 and was expected to cost $9.4 million annually for the next four years. Asked if the funding had changed, Mr Ryall said this financial year boards were paid quarterly, based on their performance towards the targets.
