They also fear that areas in Northern Ireland that lose out overall under prevalence changes will see cash disappear to other regions rather than being reinvested locally.
The four health boards shifted into a single organisation with effect from 1 April this year.
Northern Ireland GPC chairman Dr Brian Dunn said: 'Funding was supposed to stay in board areas and be recycled. With the move to one board we will have to discuss how that works.'
Western LMC secretary Dr Tom Black hit out at the GPC over the prevalence deal: 'This was politically inept and practically incompetent. In political terms, you don't bring in something with winners and losers.'
He also told the conference that 'soft terms', which failed to oblige boards to support prevalence losers, were inadequate.
He told GP newspaper: 'We have approached the existing board and I am hopeful of a soft landing for practices for one or two years.'
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