GP partners in England earn nearly 25 per cent more than their Scottish counterparts, latest figures show.
Data on GP pay from the NHS Information Centre show the average GMS or PMS partner in England earned £111,566 in 2006/7, while those in Scotland earned £22,098 less - £89,468.
Partners in Northern Ireland earned £93,316 on average, and GPs in Wales earned £97,772.
Excluding partners at dispensing practices, GMS and PMS partners in England earned £107,894 in 2006/7, while their Scottish equivalents earned £87,833. Non-dispensers in Wales earned £94,681 on average, but the figure is not available for Northern Ireland.
GPC Scotland chairman Dr Dean Marshall said the GMS contract did not address Scotland's higher rates of disease.
'We have people with higher rates of disease in Scotland, and our pay should reflect that,' he said.
'We have smaller list sizes on average, but it doesn't mean we are not doing more work.
'Unfortunately, the new contract has not addressed this and, in fact, has made the gap between the countries worse.'
Income fell for GPs across the UK in 2006/7 for the first time in a decade.
Profits in Northern Ireland appear to be falling fastest, with GMS and PMS income dropping by 5.4 per cent to £93,316 in 2006/7 compared with the previous year.
UK-wide figures reveal PMS partners' profits fell by less than their GMS counterparts, dropping 1.5 per cent to £118,499 in 2006/7. The average GMS partner's income fell 2.6 per cent to £103,530.
The average income of salaried GPs in the UK was £53,940, with little variation between countries.
Breakdown by SHA shows GP partners in NHS South West have the lowest income in England at £98,356, partly due to having the highest expenses in the country.
Dr Marshall predicted that, when figures for 2007/8 are available, they will reveal even bigger drops in profits across the whole of the UK.
'In that first year (of pay freeze), practices could try to be efficient and cut their expenses - but you can't keep doing that forever.'