The 4% fall puts further pressure on the government over its September 2015 pledge to increase the GP workforce by 5,000 full-time equivalent doctors by the end of the decade.
The total full-time equivalent GP workforce in March 2018 was 33,574, compared with 34,914 two years earlier.
GPC chair Dr Richard Vautrey told GPonline that the continuing decline in GP numbers was 'hugely concerning'. He said: 'We are going backwards rather than forwards in terms of the promised 5,000-GP expansion - and this backwards trajectory comes at a time when the population is increasing.'
Excluding registrars, retainers and locums, figures published by NHS Digital on Wednesday reveal a total full-time equivalent workforce of 27,773 in March 2018, a 1,260 fall compared with March 2016. This represents a 4.3% drop in just two years.
Numbers of GPs in partnership roles continue to drop sharply, the latest data reveal. In March 2018 there were 22,593 GP partners, down 6% compared with March 2016 - showing that 1,563 partners were lost to general practice over this 24-month period alone.
The figures also show that around a third of GPs are aged over 50 years old - and excluding registrars, retainers and locums the figures suggest that close to two out of five GPs are aged over 50.
At a time when early retirements are soaring, the data suggest that a significant proportion of the workforce could soon choose to call time on their careers. A government health minister admitted last month that GP early retirements had doubled since the start of the decade.
Dr Vautrey said falling GP numbers were affecting practices' ability to recruit, which in turn meant patients finding it harder to book appointments.
'We need expansion of the workforce - and although we are working with the government on the partnership review, indemnity and other issues, ultimately we need more investment going into general practice and the ability for GPs to use that resource to compensate for rising workload pressure.'
The BMA has warned that even with GP Forward View funding, general practice is set to be £3.4bn short of the share of NHS funding it needs by 2020/21.
Dr Vautrey said additional funding for general practice could pay for short-term measures such as bringing in other health professionals to take on some of the workload burden - such as pharmacists, physicians' assistants and non-clinical staff to take some of the administrative workload off of GPs.
He warned that it was vital to address workload pressures to make the profession 'attractive to younger doctors and more survivable for experienced GPs'.
RCGP chair Professor Helen Stokes-Lampard said: ‘These figures are yet another hammer blow for family doctors, for whom going the extra mile is now the norm, and for our patients. The stark truth is that we are losing GPs at an alarming rate.
‘It is clear that substantial efforts to increase the GP workforce in England are falling short – and we need urgent action to address this. We have made great strides over the past couple of years encouraging more medical students and foundation doctors to choose general practice, but these efforts will be futile if more GPs are leaving the profession than entering it.
‘GP workload is escalating, both in volume and complexity, and the hardworking GPs we do have are burning out as we try to cope without the resources and support we need.
‘We can’t be complacent with recruitment efforts, but retaining our workforce must be the number one priority moving forward, and doing this won’t be possible without tackling GP workload and protecting the health and wellbeing of GPs.’