The "nurture classes", which have been run in 17 primaries at a cost of just under pound;300,000, were set up last year. They were targeted on P1 and P2 pupils with behavioural problems. More than 150 children were involved.
As the debate hots up over Labour's plans to jail parents for their children's misbehaviour, Willie Hart, secretary of the Educational Institute of Scotland in Glasgow, said: "Funding this initiative would be far more productive than locking up the parents of deviant teenagers."
The unions say uncertainty is clouding the project despite the fact that it has not been formally evaluated in the schools, each of which was supplied with a base resourced to the tune of more than pound;17,000 and staffed by a specially trained teacher and a support assistant.
Pupils in the nurture groups usually spend about 80 per cent of the time in the base, where the major focus is on language, maths and personal and social development. They return to their mainstream class within a year.
Teachers involved in the groups say that pupils have shown a marked improvement in timekeeping, attendance and attitude to learning. Class teachers can spend more time on learning and teaching and other children develop more positive attitudes towards the nurture group pupils.
HMI reports on two of the schools, Alexandra Parade and Barrowfield primaries, identified the nurture group as a "key strength". Teachers in the bases were praised for liaising effectively with class teachers and educational psychologists. Parents have reported that children are more eager to go to school and to do homework.
Mr Hart commented: "In view of the Executive's emphasis on social inclusion and early intervention, it is both contradictory and short-sighted that a successful project addressing behavioural difficulties at an age group where significant progress is possible should be closed down even before any formal evaluation has been complete."
He described nurture groups as "an investment with a very high return" in terms of cutting crime and anti-social behaviour. "It is verging on the absurd that something that is so successful should be discarded after one academic session", Mr Hart said.
Approached by The TES Scotland, Sister Patricia Graham, head of St Ninian's primary in Knightswood, another of the schools involved, confirmed the "positive impact" of the initiative.
"We intend to apply the benefits of the project next session and would hope that additional resources can be made available so it can be extended," she said.
A spokesperson for Glasgow City Council said: "It was made very clear from day one that this was a short-term pilot initiative which would run until June."
She said that the early indications were that it had been "a fruitful approach" and added: "How we progress and develop the strategies it involved will be a matter for discussion over the next few months."