Sir Peter Williams, chairman of the Advisory Committee on Mathematics Education, said it might be difficult to provide the same standard of support across England and that the scheme would cost almost pound;100 million a year.
The maths intervention programme, to be known as Every Child Counts, is one of Gordon Brown's defining education policies. The Government has pledged pound;35 million a year for it, with schools expected to provide other funding from their budgets for personalised learning.
Sir Peter's comments, delivered at a National Centre for Excellence in the Teaching of Mathematics conference in Birmingham, come at an early stage in the review, which started in September and is due to conclude in June.
The Government promised in September to offer one-to-one tuition in maths and reading, with pound;144 million allocated by 2011. By that time, 30,000 7-year-olds should be benefiting from the maths help each year.
Sir Peter said he had uncovered considerable success in existing maths intervention schemes, which are often called numeracy or mathematics recovery. However, he said there was "variability in delivery" and it was "perhaps unrealistic to expect the same programme to deliver uniform results nationally".
He cited an unnamed primary school in east London where it cost pound;3,000 per pupil per annum, against the normal budget for a child's entire education of pound;5,500 a year. He said this implied a national cost of almost pound;100 million a year.
"Can we afford this?" he asked. "It depends on Government priorities. But can we afford not to intervene?"
Jean Gross is director of the Every Child a Chance charity, which is running Every Child Counts in partnership with the Government and the Primary National Strategy. She said pound;2,400 per pupil was a more realistic figure, which suggests a national annual sum closer to pound;75 million.
"Sir Peter is absolutely right to flag up that helping the very lowest attaining children does cost money," she said. "The task of Every Child Counts over the next few years is to make it work in a way that schools and the Government can afford."