Call handlers staffing an out-of-hours GP service run by the private contractor Serco have been told to make new checks before calling 999 when they receive what appear to be emergency cases in order to cut down the number of referrals they make to the ambulance service.

The Guardian has also seen a management email to staff describing how they should manipulate their computer system in order to meet targets set down in the company's contract on 999 responses.

Serco introduced a new cost-saving NHS IT system to the out-of-hours service it runs in Cornwall last summer as required by the local commissioners, enabling it to replace skilled clinicians with call-handlers without medical training who follow a computer-generated script to assess patients. The move triggered a fourfold increase in ambulance call-outs.

An email from Serco managers to staff this month, leaked by a whistleblower to the Guardian, instructed call-handlers to "stop the clock" if the IT system reaches a screen telling the operator to make a 999 call while they check it. Staff have expressed concern that this might delay an ambulance in a real emergency and that the new system is not sophisticated enough to distinguish between urgent and less serious cases.

The Guardian revealed last year that whistleblowers believed the company was putting patients at risk and falsifying data. Suspicions over the service will be raised again by these latest revelations.

There are also new allegations that the company is running the service with too few staff to operate safely. In the most recent case, over the weekend before Christmas, 22-23 December last month, a whistleblower has told the Guardian that some patients and doctors trying to call the service abandoned their attempts because they could not get through.

The local NHS primary care trust confirmed that it would ask auditors to verify the call-handling records in question and is investigating what went wrong in December.

The Serco managers' email appears to instruct staff on how to manipulate the way it records 999 cases in order to make sure it does not miss the performance targets on which it is paid.

"Please be aware that once the disposition screen for a 999 response is reached, we have three minutes in which to close the call and phone South Western ambulance service trust," it says.

"If the call remains 'open' for longer than this three-minute window we fail on our KPIs (key performance indicators). If you do not want/cannot close the call immediately … please click back to the previous screen and 'change answer' as this in essence stops the clock," the email continues.

In an effort to cut the increase in numbers of ambulances being called out, Serco has introduced a "floorwalker" who is a nurse or doctor, and has instructed its call handlers to check with them first whether the patient really is a 999 case, making it more likely that the three-minute target could be missed.

Serco admitted that the service had seen a rise in ambulance callouts when the new call-handling system was put in place and that the email had been sent by its managers, but said it was "poorly worded", "misleading" and "inaccurate".

It denied that staff had been asked to stop the clock or change performance measures. Paul Forden, Serco's managing director of clinical services, said: "The system tracks the time starting from completion of the clinical decision until the transfer to the ambulance service. The systems do not in any way change the performance that is reported to the PCT; they actually ensure more accurate reporting and all of these measures are taken in a completely open manner with the agreement of the PCT and the South Western ambulance service NHS trust. Patient safety is absolutely at the heart of this service."

The Cornwall PCT that awarded and monitors the contract said it would never agree to changes being made to the way calls are recorded in the manner described in the email, but that it had been assured by Serco that it was not in fact "stopping the clock". Bridget Sampson, its director of primary care, said the PCT had approved the introduction of clinical staff to overrule the system to ensure emergency services are reserved for those in most need.

The PCT also confirmed that an investigation was under way into call response times over the weekend before Christmas. It confirmed that Serco was treating the issue as a "serious incident" and had been asked for a full report.

Serco said allegations that it did not have enough staff the weekend before Christmas or that patient calls were abandoned were not true. It said there had been an unpredictable surge in demand for services across Cornwall over the period, with out-of-hours receiving double the number of calls it took the previous year. It added that it had completed its own report, which had confirmed there were no problems.

The South Western ambulance service NHS trust declined to comment on the Serco email, but said that teething problems with the new call triage system had been addressed collaboratively with Serco and the PCT so that 999 referrals were now swift and appropriate.

Following the Guardian investigation into Serco, the health watchdog the Care Quality Commission (CQC) found serious failings in the service last July. It carried out a further unannounced inspection in December to see if the failings had been rectified. The National Audit Office has also been investigating data manipulation and the PCT's ability to monitor its contracts at the invitation of the powerful House of Commons public accounts committee. A third independent audit of Serco's reporting to the NHS was commissioned by the PCT from the accountants PWC following the Guardian's revelations. All three reports are expected shortly.

The MP for West Cornwall and the Isles of Scilly, Andrew George, who reported Serco to the CQC, called for changes in the way private companies were allowed to report their performance to the NHS. "It is time to recognise that it is no longer appropriate that companies effectively control their own data collection and evaluation," he said.