An exodus of about 1,000 dentists from the NHS in England was predicted last night by the chief executives of primary care trusts, who take over management of the service from today.

The NHS Confederation provided the first hard evidence of how patients will be affected by a dentists' contract that came into effect at midnight.

It said PCT chief executives forecast that 6% of dentists will stop providing free NHS treatment for adults over the next 12 months and 5% will withdraw NHS treatment for children.

Nearly 20,000 dentists were paid for NHS work last year, according to official figures from the Dental Practice Board. But the board's total included many dentists who also did private work and there was no reliable estimate of the number of patients who could be affected.

The confederation, representing NHS managers and trusts, said the position could change if dentists realised the benefits of the new contract, which is intended to provide better rewards for preventive work and less for "drill and fill".

The survey of 124 chief executives found there is already a shortage of NHS dentists in many parts of England.

NHS dentistry lists in 15% of PCT areas were closed for adults, making it impossible for newcomers to the area to register. For children, lists were closed in 10% of trusts.

Dame Gill Morgan, the confederation's chief executive, said media reports of the end of NHS dentistry were wrong. PCT chiefs were engaging alternative providers to maintain services in areas where not enough dentists were signing the new contract. "However, the introduction of the new contract has caused uncertainty and the confederation is calling for better communication about the benefits for dentists and patients."

The government may have to review the contract next year.

Peter Ward, chief executive of the British Dental Association, said many dentists were signing the new contract while continuing to dispute the terms.

"The profession recognised the need for change from the old system which, in the words of the Audit Commission, put dentists on the treadmill. But the new contract is target-driven and untested, and the fear is that it won't give time for more preventive care."

The health minister, Rosie Winterton, said: "All the current indications are that most of the dentists leaving do relatively little NHS dentistry, and account for only a small fraction of NHS services."