A pound;2 million early intervention project, which gave free nursery education to hundreds of the most vulnerable two-year-olds, is to lose its funding under the concordat between central and local government - before its impact has been fully evaluated.
The removal of funding from the three authorities piloting the initiative means it will not now be rolled out across the country.
Scottish Government officials have told North Ayrshire, Glasgow and Dundee councils that their funding for 900 nursery places for toddlers will cease in June, because the new financial arrangement removes ring-fenced funding for specific initiatives.
The decision is likely to be seen as flying in the face of the SNP administration's promise to "tackle early the things that hold children back in later life".
Early years practitioners have also expressed surprise that the decision has been taken before researchers at Strathclyde University publish their evaluation of the scheme in September.
Fiona Hyslop, the Education Secretary, told The TESS that local authorities could still fund the places if they chose, but added that removing children from failing parents might not be in their interests.
"Some people might say that to take a child away from its mother and into nursery aged two is not necessarily a good thing," she said.
However, Margaret Curran, who launched the scheme in 2006 when she was Communities Minister, countered: "These projects were deliberately designed to target children in need of additional care and support. For them, things were not working at home.
"I would have real concerns about any decline or closure of these services, because the way to tackle child poverty is to intervene as early as possible."
In North Ayrshire, the two-year pilot has allowed the council to provide 100 half-day nursery places five times a week for two-year-olds deemed "at risk", often because of their parents' mental health or addiction problems.
Johanna Brady, the council's childcare strategy manager, commented: "Research has shown that, if vulnerable children are not given the care and stimulation they need, by the age of three they can be as much as a year behind other children in their development."
In Dundee, the 102 places for two-year-olds have been credited with improving their social skills and ability to integrate.
Lisa Woolfson, an early years expert at Strathclyde University who is evaluating the project for the Government, said it was too early to gauge its effectiveness.
However, Dr Woolfson claimed: "You would find it hard to find someone arguing against the idea of providing early education to vulnerable children in that age group."