Heads are concerned for the future of projects to boost the achievement of disadvantaged pupils as the three-year Raise initiative (raising attainment and individual standards in education) comes to an end.
Hundreds of schools have benefited from the Pounds 40 million scheme, launched by the Assembly government in 2006 to target about 20,000 children living in relative poverty in Wales.
Grants awarded to primary and secondary schools where at least 20 per cent of pupils are eligible for free school meals (FSM) have been used to fund literacy projects, nurture groups and after-school clubs.
But heads of smaller schools fear these projects will suffer when the funding dries up next year.
Nantymoel Primary in Bridgend, which has 25 per cent FSM, used Raise to employ a classroom assistant to give extra support to underperforming children.
Head Jeff Roberts said he had been forced to run a "watered down" version of the scheme next year.
"We will employ the classroom assistant through our main budget, but she will not use her expertise specifically with children in Raise groups," he said.
The Assembly government insists Raise funding had a clear life-span and has set up a website to help schools share good practice.
But a final report on Raise published by Estyn last week said there was concern that schools had not planned to make their projects sustainable for the future.
It found that although individual pupils benefited from Raise-funded projects, most schools targeted their less able pupils rather than those from the poorest backgrounds.
As a result, the prospects for the most disadvantaged pupils did not improve over the three years of the scheme. Last year, less than one third of children eligible for FSM in Wales achieved five A*-C grade GCSEs.
Meilyr Rowlands, managing HMI at Estyn, said: "We knew the initiative would be for a certain period of time. The idea was to pump-prime good ideas that could be used in schools that didn't get Raise funding."
But Mr Roberts said "economies of scale" made the withdrawal of funding from small schools, such as his, difficult.