GP leaders warned that the data showed the extent of the crisis facing general practice in England, with doctors retiring early to escape unmanageable workload.
In 2015 there were 34,055 full-time equivalent GPs in England excluding locums, down 657 (1.9%) from the 2014 estimated total, data from the Health and Social Care Information Centre (HSCIC) show.
Full-time GP numbers excluding locums, retainers and registrars fell even faster - dropping 3.2% to 29,271 in 2015 - a fall of 980.
Headcount figures showing the total number of GPs in England - excluding locums - also fell to 40,697 in 2015, down 408 (1%) from 2014, the HSCIC data reveal.
Despite the RCGP hailing a surge in GP trainee recruitment in 2016 as evidence of a 'turning tide' in GP recruitment, the latest official data are a blow to health secretary Jeremy Hunt's pledge to recruit and retain 5,000 extra GPs by 2020.
The government remains committed to the pre-election pledge, with NHS England unveiling £206m plans to achieve the promised rise in GP numbers in its GP Forward View document last week.
A DH spokeswoman said: 'We are committed to our target of 5,000 more doctors in general practice by 2020. NHS England is taking action to double the growth rate in GPs through new incentives for training, recruitment, retention and return to practice.
'NHS England’s GP Forward View, which commits an extra £2.4bn for general practice by 2020/21, will help to reduce the pressure on GPs and retain a healthy workforce well into the future.'
The workforce data also show that the proportion of GPs who are women continued to rise in 2015. A total of 54.4% of GPs were women in 2015, compared with 52.4 in 2014 - up from 42.5% in 2005.
Just over one in five GPs (20.8%) was aged over 55 in 2015, the data show - a slight decrease compared with the previous year. In London, however, nearly one in four GPs are aged over 55.
Data on practice staff included in the workforce report show that numbers of nurses employed in primary care rose in 2015 compared with the previous year, while other staff - including admin and non-clinical staff, fell.
GPC deputy chairman Dr Richard Vautrey said: 'These figures further expose the crisis in general practice with GPs leaving because of unsustainable workload pressures.
'It is deeply worrying that at a time of escalating patient demand, especially from an ageing population, there has been a decrease in the number of GPs and staff focused on delivering patient care. The public is already seeing the impact of this in their local GP practice, with many struggling to provide enough appointments.
'Ministers cannot wait a moment longer and need to ensure that its recent promises of new funding to GP practices materialise as quickly as possible.'