Pay for GPs in Northern Ireland fell by over 5 per cent while GPs in Wales saw their income dwindle by 4.3 per cent.
An average GP in Northern Ireland took home £93,316 in 2006/7, while in Wales the figure was £97,772.
The pay gap between England and Northern Ireland widened to over £18,000.
Dr David Bailey, chairman of GPC Wales, said the disparity was due partly to extra investment in England compared with the rest of the UK, and partly due to extra expenses.
Welsh practices lost out on enhanced services funding last year after the Welsh Assembly Government withdrew funding for them following a disagreement with GP leaders.
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