The government's programme to promote fruit and vegetables in schools has been hit by a freeze on health spending and by an official evaluation that suggests it has made little significant impact on children's consumption.

Staff managing the five-a-day healthy eating promotion and school fruit and vegetable schemes - Labour's most important public health scheme to date - have been left in limbo since the Department of Health imposed a moratorium on all new programme expenditure last autumn. Most of the staff are on contracts that expire in March and with no certainty about future funding, many have left for other jobs. Reports suggest half of the five-a-day coordinators in London have moved on, and school coordinators around the country are also looking for other work.

The national school fruit and vegetable scheme provides a free piece of fruit or vegetable every day to nearly 2 million children between the ages of four and six in more than 16,000 schools. It forms part of the government's strategy to tackle obesity, heart disease and cancer by changing people's diets. The total cost of the school fruit and vegetable scheme in 2004-05 was £29m, and is expected to be £37m in 2006-07.

The Department of Health said this week: "In the short-term, coordinators' contracts will be extended for at least three months beyond the end of this financial year while long-term plans for this important scheme are put in place."

The contracts freeze was introduced in November as part of an embargo on all new spending commitments. A department spokesman said the general freeze had been lifted, but no statement was likely about the result of spending reviews. "We will not be giving a running commentary on individual spending plans in the department," he added.

The health secretary, Patricia Hewitt, will promise in a white paper on Monday to double the budget for health promotion over the next 10 years. Evidence that the programme was being disrupted by financial chaos in the NHS might have upset the launch of the white paper. Programme coordinators said they had not yet been informed of the change of heart.

The fruit and vegetable scheme is highly popular with parents and schools but an official evaluation found it has had no lasting effect on children's consumption of healthy food. Children eligible for the free fruit or vegetables increased their overall consumption by an average of only one third of a portion a day, failing to reach the government's five-a-day target. Experts say they warned the government that without funding for educational programmes to support the scheme it was unlikely to achieve much.

The Department of Health said: "Children participating in the scheme ate more fruit and vegetables than those not in the scheme, plus there was an increased awareness and knowledge of the five-a-day message. We know more work needs to be done to continue raising awareness of the importance of healthy eating but changing behaviour can take time."

Dr Martin Caraher, food policy expert at London's City University and adviser to the Department of Health, said the scheme had failed to address wider issues about children's diets: "We warned the Department of Health that international research showed that simply making free fruit available in schools was not enough."

Professor Fergus Lowe, who has run the successful Food Dudes programme from the University of Wales to change children's eating habits, said the school fruit scheme was unlikely to be effective without a broader educational programme. "It won't deliver the benefits required unless a serious effort is made in other ways to change children's habits and attitudes."