Childsmile involves staff at all Scottish nurseries offering free supervised toothbrushing every day.
Glasgow researchers found that the scheme had reduced the cost of treating dental disease in five-year-olds by more than half between 2001 and 2010.
The programme was launched in 2001 and costs about 1.8 million pounds a year, the BBC reported.
It emphasises the importance of toothbrushing and helps parents establish a healthy diet from the earliest stage.
A number of nurseries and schools in targeted areas also provide fluoride varnish and toothbrushing in primary one and two.
There was also said to be a drop in the number of children needing hospital treatment for dental problems, freeing up operating theatres.
Public Health Minister Michael Matheson said: "This is an amazing achievement and shows just how much can be saved from a very simple health intervention.
"This has seen less tooth decay in children which means less toothache, fewer sleepless nights and less time off school.
"By this simple measure, National Health Services costs associated with the dental disease of five-year-old children have decreased dramatically.
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