Figures published last week show that 6,700 fewer three and four-year-olds took up pre-school nursery provision in the last school year, compared to the previous one.
A spokeswoman for the Executive said first indications suggested that the drop was simply down to parental choice.
However, it plans to ask councils whether the short nursery hours offered in the majority of local authority nurseries may be a factor. It also wants to discover whether the nursery nurses' industrial dispute from 2003-2004 has had an impact on uptake.
The Executive's annual census showed that 81 per cent of three-year-olds and 97.8 per cent of four-year-old were registered in 2005. The previous year, 85 per cent of three-year-olds and 100 per cent of four-year-olds were registered with pre-school education centres.
A spokeswoman for the Executive said: "Nursery education is optional and it is for parents to decide what is best for their children. However, we would encourage parents to make the most of free provision."
She added that the figures were still healthy and Scotland was ahead of the UK's participation rate.
Fiona Hyslop, the SNP's education spokesperson, said the current statutory provision was less than 11 hours per week.
"The SNP wants to increase this to a full half-day as one of the first steps on the road to a comprehensive package of childcare and early-years learning measures."
The latest statistics also revealed another challenge to the Executive's pre-school ambitions. There were 6,100 childminders in Scotland in January 2005, which is a slight decrease from 6,165 in 2004. But more significantly, almost 18 per cent of childminders had already left or intended to leave childminding in the next year.
Other points from the census include:
* Forty-nine per cent of childcare and pre-school education centres are local authority-managed in the most deprived areas, compared to 35 per cent in the least deprived areas;
* there are 1,984 childcare and pre-school education centres run by local authorities, 1,037 privately-run centres, 1,345 voluntary centres and a further 351 centres of unknown management types;
* 2,517 of the centres offered a nursery service, 1,079 an out-of-school club service, 368 a breakfast club service, and 62 had Gaelic provision.
* the number of pre-school education staff stood at 12,573, of whom 17 per cent were registered with the General Teaching Council for Scotland.