Average income before tax for partners and salaried GPs across the UK in 2016/17 was £92,500, up from £90,100 in 2015/16, figures from NHS Digital show.
For partners, pay rose by 4.1% to an average £105,500 across the UK, while salaried GPs saw a 1.7% increase in 2016/17 to an average of £56,800.
GPC chair Dr Richard Vautrey said the latest income figures showed contract agreements in recent years that have brought additional investment were 'starting to deliver'. The 2016/17 contract deal for England agreed by the BMA, the government and NHS leaders promised £220m in additional funding.
However, he warned that 'a significant proportion of the apparent rise' in income for partners was likely to have been triggered by the rapid fall in numbers of GPs, leaving practice funding spread between a smaller number of increasingly stretched doctors. The overall GP workforce has fallen by around 1,400 GPs since September 2015 - and numbers of partners dropped by around 800 in the 2016/17 financial year alone.
Dr Vautrey added that GPs had still seen real-terms pay fall by almost a quarter over the decade to 2016/17 - and that expenses were at an all-time high as a proportion of gross income for practices.
Income rose faster in England than in other UK countries in 2016/17, rising 3% to £93,700 across all GPs, and by 4.6% for partners in GMS and PMS practices to an average of £109,600.
Average income rose by just under 2% across all GPs in Scotland and Wales, while Northern Ireland was the only nation that saw pay fall - with average income across all GPs down 1.3% to £87,700 in 2016/17.
Dr Vautrey told GPonline: 'After a decade of pay cuts, as demonstrated in this report which shows that GPs have had a real-terms cut in pay of 23.1% since 2006/7, these figures provide signs that the contract agreements we have recently made are starting to deliver for GPs.
'However we need to treat this information cautiously as it coincides with a large fall in the number of GPs and, with practices often struggling to find GPs to replace those leaving the practice, it has often meant those GPs remaining picking up the extra workload and so working longer more intense sessions each day.
'With partners unable to hire more doctors, they themselves are taking on additional work, are forced to work longer hours and are placing further pressure on themselves to deliver care to patients amid mounting demand.
'It is likely that the falling workforce accounts for a significant proportion of the apparent rise in an average partner’s salary. This increase in payments does not compensate for a working environment that is often proving unsustainable.
'The expenses to earnings ratio is now at an all-time high and is evidence that practices are both investing in practice staff but also that they are facing huge cost pressures to keep their practices running. This is something the partnership review needs to take in to account.'
Dr Vautrey added that the BMA was waiting to find out how a £20bn increase in NHS funding over the next five years promised by the government would 'lead to investment in the general practice workforce and how it will address the serious problem of unsafe workloads'.