Delegates at the conference in Enniskillen on Sunday 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.
GPC Northern Ireland chairman Dr Brian Dunn said 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 global sum, in Northern Ireland they were not.
A £13m ‘pot' has accumulated and the assembly government cannot work out the exact amount owed to each practice, said Dr Dunn.
‘We don't know why, but the government says various superannuation forms had not been signed. But GPs know what they have paid their staff, they've got records, so we don't know why,' 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.
Read the full story in this week's issue of GP newspaper dated 26 March.