The department will not renew its contract with the site's supplier when it expires on 31 October, meaning GPs will have to apply to PCTs for funding or pay to maintain access.
But some PCTs said they will not pay the subscription fee, expected to cost up to £100 each year. A spokeswoman for NHS Birmingham East and North said: 'Given the current financial pressures upon PCTs it is unlikely the trust will purchase access to the toolkit for all GPs.'
North Yorkshire LMC member and GP Dr Shaun O'Connell said: 'It's a nuisance that the news has come part way through an appraisal year. It's not a long process to download previous information but it's inconvenient.'
Earlier this year, the DoH suspended access to the toolkit after it emerged the site was vulnerable to hackers. This was not related to its decision to cease funding, the DoH said.
After the contract ends, GPs who do not subscribe should have a year to download their data before it is deleted.
The DoH said its policy was that arrangements for appraisals should be made locally.
A spokesman said: 'It would not be right for the department to continue to hold a contract with one provider or to fund one particular system centrally.'