GPC Wales asked Welsh government health officials last month to supply a breakdown of local health board spending on enhanced services and primary care organisation (PCO) administered funds.
LMCs are concerned these flexible elements of GMS funding are being used by health boards to fund other services or to hide costs that should not have been allocated to the GMS budget.
GPC Wales deputy chairman Dr David Bailey called for the figures to be released by next month so LMCs could identify where funds are being spent correctly or incorrectly.
While the government had been 'fairly open' in sharing national data, Dr Bailey said, local health boards had been 'reluctant' to release spending data to LMCs. 'I wouldn't like to speculate,' he said, 'but I think the average GP will probably have their suspicions.'
Funding for enhanced services and PCO administered funding, which includes maternity and other discretionary payments, could add up to almost 20% of total GMS funding in Wales, with enhanced services accounting for about £37m.
Dr Bailey said the main concerns were that money was being cut when health boards 'want to save money for elsewhere', and used to 'hide costs which should never be allocated to the GMS budget in the first place'.
'Things like administrative costs for the PCO, they're being taken out of GMS monies,' he said.
'In enhanced services, there's a suspicion a significant chunk of that money is going to secondary care services to pay for things they should be funding themselves.
'Things like wound care services that were devolved to West Wales GPs, then taken back and provided by the hospital again. So they are being paid for doing something they should have been doing in the first place.'
GPC Wales wants figures broken down and shared with LMCs, said Dr Bailey, 'so we have more chance of identifying where people are playing ducks and drakes with the way funding is allocated'.
A Welsh government spokesman said GPC Wales' request for data was 'currently being progressed'.