Staff at the Cornwall out-of-hours GP service have raised fresh concerns this week about the care being provided by the privatised contractor Serco over the jubilee bank holiday weekend, as new sources came forward to the Guardian to allege that data tracking Serco's performance has been regularly altered in order to meet targets that the service has in fact failed to meet.

The Serco service is currently being investigated by the health watchdog, the Care Quality Commission, over allegations that it has been so understaffed as to put patient safety at risk and over claims that data has been manipulated. The Guardian revealed last month that the privatised service, to which the Cornwall NHS primary care trust outsources, had received an unannounced inspection from the regulator.

Subsequently, during the four-day jubilee weekend, sources say the service was again so understaffed, despite being under scrutiny, that large delays built up in dealing with patients. In one case, a professional carer calling in for a repeat prescription on behalf of a terminally ill patient waited just under six hours for a clinician to call them back. By the time the doctor on duty returned the call, the patient had died. In a separate incident, a call classified as needing an emergency home visit, which must be made in less than one hour to meet standards, was recorded in the logs as receiving a visit nine minutes after the deadline.

Serco denies that its service is unsafe and says that it is meeting the terms of its contract with the local PCT, which allows it to report adjusted performance figures when patients are to blame for delays.

The CQC investigation comes as the NHS undergoes radical restructuring. Under coalition policy, all 52 newly formed PCT clusters in England are required this year to identify at least three of their community services to put out to competitive tender in a process that will lead to a rapid increase in private-sector involvement in the NHS. Critics have questioned whether NHS services should be run for profit and whether commissioning bodies have the ability to monitor contracts.

Serco, which generated revenue of £4.6bn in 2011, is likely to bid for many of the NHS contracts, based on its Cornwall performance.

Its medical director in Cornwall, Dr Jeremy Mawer, said he had investigated the two cases that arose over the holiday weekend. In the first case, he acknowledged that there was a "regrettable" delay in calling back "due to a very high call rate". "Sadly, the patient died, but this was certainly not contributed to by the delay in returning the phone call. The patient died quietly with full symptom control. They did not run out of drugs at any point and there was no danger of this happening."

In the other case, Serco denied that an emergency home visit missed its deadline. Dr Mawer says the company's car tracking system shows that the doctor's car was on the scene 50 minutes after the receipt of the call, within the one-hour deadline. Asked to comment on the apparent discrepancy between the car tracking and the official log recording when the doctor had started the visit, Serco categorically denied verbally that the logs at any point showed that the call was dealt with nine minutes after the deadline, but declined to confirm the denial in writing. The Guardian can confirm, however, that the logs did record the call as failing to meet its deadline by nine minutes.

The computer log recorded the call being assessed as an emergency by one of two doctors who monitor the contract for the PCT while also working shifts for Serco, at 14:35.53, at which point the clock was started, giving it a "less than one hour" deadline. The log then records a second GP, Dr Rob White, who also combines shifts at Serco with monitoring Serco for the PCT, as beginning a home visit at 15:45.00, 69 minutes and seven seconds later, after the deadline.

Dr White told us that although he was logged as making the visit to the emergency case, it was not in fact him but a registrar he was training who made the visit while he was visiting someone else in the same road at the same time. He said he assumed the registrar entered the times of the visit when it had finished and would have logged in as Dr White because they did not have their own access privileges. He added that the outcome of the visit was changed from fail to pass because a doctor was at the scene within the target time.

New sources who have spoken to the Guardian and to the regulator as part of its investigation have alleged that they witnessed regular alterations of data for reports to the PCT, with call and response times being altered in order to allow failed outcomes to be logged as passes. The CQC is expected to report on its investigation, which began in April, in the next few weeks. It has told us that it has not carried out a forensic investigation of computer logs.

The PCT said it would conduct its own review of the cases raised by the Guardian and declined to discuss whether it allowed such alterations before it was complete. Dr Colin Philip, chair of Kernow Clinical Commissioning Group, said: "During the four-day jubilee break, Serco gave assurances about substantial increases in their staffing levels. Despite this, we understand there were some delays in how quickly some patients were triaged.

"We are in discussions with Serco about the reasons for this, as patient safety is our key priority." He added that he believed that the majority of patients received a good service from Serco clinicians and that feedback surveys confirmed this.

"We await the CQC report and will seek further independent assurance if the scope of [our] initial audit needs to be widened."

Serco denied that any data had been manipulated and told us that an independent audit by the PCT following earlier allegations found there was no substance to any such claims. The Guardian has learned that the PCT audit, conducted by its internal auditors, did not carry out a forensic analysis of the underlying logs to see if data had been altered.

Serco's managing director of clinical health, Paul Forden, said: "Serco increased staffing levels for the jubilee weekend by over 18% compared with a normal four-day weekend to cover the anticipated increase in calls. 100% of urgent calls and visits were dealt with within the required timeframes. We remain fully committed to providing the best possible care for patients."