GPs are paid seniority based on their years of experience and their practice's profitability.
Practices receive an interim payment based on their estimated profits because superannuated profits are not known until after the financial year ends.
But a number of east London practices say they have been underpaid because City and Hackney PCT underestimated their profits. The PCT has told them it is unable to make up any shortfall for previous financial years.
Dr Richard Vautrey, GPC deputy chairman, said that any practice that was not receiving its full entitlement should consult its LMC. 'PCTs are obligated to pay the full amount of seniority payments,' he said. 'They have the money, and should make arrangements to pay it.'
The manager of one practice in Hackney said she first noticed the shortfall in July. When questioned, the PCT said the full payment was being withheld because each partner was earning less than two-thirds of the national average for GPs.
'It was difficult to find out where it had got those figures from,' she said. 'Nobody seemed to be able to do anything - it was as if the computer's in charge, and that's it,' said the practice manager.
The practice has since provided more accurate figures for its profits, and has seen its payments for the current financial year increase.
It is still owed about £9,000 from 2006/7, because there is no mechanism for reclaiming payments from previous years.
Four nearby practices have experienced similar problems.
Laurence Slavin, a medical accountant with Ramsey Brown, says he is aware of practices that have suffered similar problems in other parts of the country.
'This isn't a local one-off problem. It's more systemic than that,' added Mr Slavin.
A City and Hackney PCT spokesman said that seniority payments were a national issue and that because a number of practices that have failed to return their profit declarations since the 2004/5 financial year it was not possible to make final calculations.
'GPs earning £63,556.66 per annum or above automatically receive 100 per cent seniority,' she added. Other GPs have to wait until their annual certificate of pensionable profits were received and adjusted against national average earnings when the figure was available.
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