The NHS Appraisal Toolkit website will be closed until the first week of March, meaning GPs will be required to submit appraisals by post or delay returns.
GPs make up the majority of 15,000 users scheduled to complete appraisals before the end of March, according to the Sowerby Centre for Informatics at Newcastle (SCHIN).
The DoH has asked PCTs in England for flexibility on the appraisal deadline, after GPC chairman Dr Laurence Buckman asked for it to be extended.
'In normal circumstances, all GPs are expected to have completed their NHS appraisals by 31 March each year,' said Dr Buckman in a letter to health minister Mike O'Brien.
'However, the fact that many GPs will have to re-arrange their appraisal, potentially with a backlog occurring after this period, means that it is likely that many GPs will be unable to meet this deadline.'
A routine security check recently discovered the appraisal website could be compromised by intruders and it was quickly shut down by ministers.
The DoH said the website, established nine years ago, was 'not sufficiently robust to withstand modern day hacking'. There was no evidence of a security breach or loss of data.
The GPC has urged the DoH to meet any extra costs to appraisers or appraisees.
Dr Buckman has also asked that 'it be ensured that the toolkit is not relaunched until the full security of doctors' data can be assured'.
The DoH would not confirm the cost of bringing the service back online, however, nor whether the government would foot the bill for any extra expense incurred by GPs.
A spokesman said he did not expect doctors to be penalised.