Delegates at the conference in Enniskillen last weekend were told that a formula, based on practices' MPIG, would have to be used to distribute two years' worth of staff superannuation funding to partners.
Northern Ireland GPC (NIGPC) chairman Dr Brian Dunn told GP many practices were owed between £30,000 and £40,000 after Northern Ireland's government changed the way practice staff superannuation was funded in 2008.
While payments were matched by the treasury in England, Scotland and Wales via the global sum, in Northern Ireland they were not.
A £13 million 'pot' has accumulated and the assembly government cannot work out the exact amount owed to each practice, said Dr Dunn.
'The DoH says various superannuation forms had not been signed. But GPs know what they have paid their staff,' he said.
A motion was passed calling for a formula based on MPIG to distribute the cash, and deploring the lack of information available to GPs in Northern Ireland about their pensions.
'The best way to do it is to model it on MPIG as that gives a fair reflection of practice staff. Practices with higher MPIGs generally have more staff,' said Dr Dunn.
Dr Tom Black, deputy NI GPC chairman and medical secretary of the Western LMC, said 50 per cent of practices would lose out.
'There will be winners and losers, with some practices receiving less money than they have paid out to their staff,' said Dr Black.
Dr David Ross, treasurer of Eastern LMC, said it was a 'disgrace' GPs in Northern Ireland could not get accurate information on pension contributions.
'GPs approaching retirement are left not having a clue what their pension will be,' he said.
UK GPC chairman Dr Laurence Buckman said he 'cannot believe' the correct superannuation contributions could not be calculated by the country's government.
'In England they push a button and you can get an update whenever you want,' he said.