Figures show health boards, including Glasgow's, are falling significantly short of government targets for fluoride varnishing.
At least 60% of three and four-year-old children should receive at least two applications as part of the 'Childsmile' programme.
However in NHSGGC, the uptake rate was 40% and 35%, in the areas with the highest deprivation, and dropped as low as 8.1% in more affluent areas.
The figure for NHS Lanarkshire was between 39-42% in the most deprived areas and 12.28% in less deprived parts.
Dental decay is almost totally preventable but is the single most common reason to admit children to hospital in Scotland. Research has shown a link between poor gum health and heart disease in later life.
NHSGGC said it would continue to encourage dentists to participate in the Childsmile programme and said it was providing fluoride varnish applications to an increased number of nurseries this year in 'high risk' areas.
Children are offered a further two applications in priority nurseries and schools.
A spokeswoman for NHSGGC said: "It is recognised that tooth decay is higher in populations of high deprivation so we have been working to provide this service in population areas where it is needed most.
"This approach ensures fluoride varnish application is targeted in our most at-risk populations and is therefore helping to address oral health inequalities across Greater Glasgow and Clyde.
"We will continue to encourage General Dental Practitioners across the whole of NHS GG&C to participate in the Childsmile Practice Programme and to provide access to fluoride varnish application to all children in NHS GGC who are registered with a dentist."
The Royal College of Physicians and Surgeons of Glasgow has called for fluoride to be added to water supplies to improve oral health.
NHS Lanarkshire said it was continuing to see improvements in the oral health of children with 64% reported as having no "decay experience" last year.