GPs are being underfunded for pension payments by tens of thousands of pounds, forcing them to dig deep into
contract pay rises to meet shortfalls.
Medical accountants said almost every GMS or PMS practice could be affected, particularly at practices with 'mega' profit increases.
Rosemary Smith, GP liaison manager from Sandison Easson and Co in Wilmslow, Cheshire, said a five-partner 'average' practice may face a shortfall of £10,000 for its own employees' contributions and £27,000 for employers' contributions.
One 'exceptionally well-performing' practice had a £120,000 shortfall, she said.
The shortfall is because the amounts practices are funded for superannuation in the global sum and PMS budgets is based on historic profits, which have now risen sharply.
'They haven't been reimbursed it's coming out of their pockets,' Ms Smith said.
Paul Kendall, a partner at Dodd and Co in Penrith, Cumbria, said superannuation was a 'big problem' and practices would be left with liabilities of up to £15,000.
Bob Senior, vice-chair of the Association of Independent Medical Accountants, said: 'All practices are underfunded for superannuation.
'Superannuation in the global sum has only been given inflationary uplifts but there have been big profit rises.'
While practices are cash rich with quality achievement money, Rosemary Smith is warning them not to increase drawings because of impending higher tax bills.
The combination means practices are effectively being taxed at 60 per cent, she said.
'When I see clients they want to take their cash now. Over 70 per cent of quality money needs to be held back for tax and superannuation.'
By Ian Cameron