The temporary closure of the NHS Appraisal Toolkit website over security fears and subsequent technical issues have delayed many GPs submissions.
As a result, the majority of PCTs have extended appraisal deadlines by up to three months.
The appraisal website was taken offline just weeks before the annual appraisal deadline over hacker fears.
But since the re-launch it has been plagued with problems over log-on access, speed and functionality.
The DoH said the site was now ‘fully functional' and its providers, the Sowerby Centre for Health Informatics at Newcastle, is undertaking updates to improve support.
However, since the security overhaul GPs who forget their password must provide documentary proof of registration to their PCT before being granted access.
An NHS Greenwich spokeswoman said: ‘This is actually causing more of a problem than the website failures.'
Information from 35 PCTs shows 83% have extended deadlines after GPs struggled to hit the original cut-off date of Wednesday (31 March).
Professor Mandy Ashton, NHS Leicester City's director of quality, said: ‘Usually appraisals must be completed by the end of March but we extended the deadline until the end of April to support any GPs affected by problems with the national web-based toolkit.'