The organisation, contracted to provide NHS 111 phone services in 11 areas, said problems with the service in two areas when it launched meant calls were being handled by other providers.
A spokeswoman for NHS Direct said payments for the first few weeks of NHS 111 contracts had not yet been finalised, but penalties were expected for failing to meet key performance indicators.
GP out-of-hours services in the West Midlands and north-west England, and an ambulance trust in north-west England, continue to handle calls that were contracted to NHS Direct.
The spokeswoman said NHS Direct was being paid only for the calls it handled. ‘NHS Direct is currently in discussion with our commissioners and NHS England about the services we are providing,' she added.
Figures published with NHS Direct’s latest board papers show the service answered just 30% of its contracted calls in April.
The figures show the service failed to meet a series of targets including call transfer times, call-back times, complaints actioned within deadlines, referrals to 999 and referrals to A&E.
Financial figures show the service had a deficit of £1.5m.
The spokeswoman said: ‘Following the launch of the NHS 111 services it was found that the length of the calls was greater than the level planned for and the number of calls referred to nurse advisors was also much greater than planned for. This has meant that not all of the targets that we would expect to meet have been achieved.’
GPC chairman Dr Laurence Buckman said the latest monthly figures released by NHS England for the whole of NHS 111, which showed a slight improvement overall, did not give the full picture of the troubled service.
He said said in many areas of the country the service was still not in operation or was reliant on support from GPs and other NHS providers.
‘This situation is placing pressure on other already overstretched NHS services that cannot afford to be diverting resources and time in order to prop up NHS 111,' he said.
'There remain significant concerns about NHS 111’s ability to deal with the volume of calls it receives and the quality of advice being given to patients.’