Cash flow problems have been reported by practices across England because of missed and late payments from local area teams and local authorities.
Funding shortages have forced some practices to breach overdraft limits, incurring bank charges or leading to banks freezing their accounts.
Practices warn that they have had insufficient cash to cover partners' drawings and could be forced to lay off staff if the problems persist.
GPs warned that if QOF achievement payments are affected in June, many may struggle to cope.
Practices hit out at staff being forced to waste time chasing payments and warned that the cascade of key health information had also been disrupted by reforms.
One north London GP, who asked not to be named, said her practice's premises and QOF advance payments were about £10,000 short in April and May. The GP said the practice bank account had been frozen after April's staff wages breached an agreed overdraft limit.
Her practice was promised an interim payment in April that 'didn't happen', and a May payment was also short. 'We were horrified to see that again it was short by about £9,000,' she said.
The GP said if payments were delayed into a third month, the practice would be forced to lay off staff.
Another London GP said his practice had been forced to ask for an overdraft to pay staff wages, triggering a bank fee. The practice was underpaid by about £30,000 in one month - close to its entire wage bill.
Medical accountants reported QOF aspiration payments or premises payments that were short or missed. Other practices received unexplained additional payments.
One accountant said one practice had not received any April payment, a scenario that would be 'critical' for most practices.
Wessex LMCs chief executive Dr Nigel Watson described multiple payment problems in his region.
Some practices are yet to receive local enhanced service payments, said Dr Watson. 'Some payments weren't authorised by CCGs because they didn't realise they had to do it, despite being told.'
Meanwhile, Birmingham LMC chief executive Dr Robert Morley said the LMC sent out MMR vaccine information because 'processes for cascading important information to GP practices are unfit for purpose'.
GPC deputy chairman Dr Richard Vautrey said the reforms had fragmented the NHS and advised practices to be 'bullish' in seeking recompense for any costs incurred.
A spokeswoman for NHS England said: 'We are obviously committed to ensuring that the right systems are in place to make payments. Where there have been transition difficulties, these will be resolved as quickly as possible. We are aware of some individual issues and these are being addressed locally.
'If practices are experiencing current difficulties, we would welcome contact with area teams so that issues can be dealt with as soon as possible.'