Barts and the London NHS Trust has apologised to 442 patients who were not seen within maximum government waiting limits because of inadequate management systems.
The patients waited an average of six weeks longer than the 13-week waiting time national standard for an outpatient appointment.
The trust said the delays were caused by inadequate management systems within the Outpatient Appointment Office.
The trust has launched a "serious untoward incident" investigation to identify the root cause of the issue and why management systems did not alert the organisation to delays sooner.
In a statement the trust said that no patient had come to "direct" clinical harm as a result of the delays.
Last April Barts and The London NHS Trust installed the Cerner Millennium Care Records Service as part of the NHS's £12.7bn National Programme for IT. After the go-live last year it had difficulty gaining an overview of which patients had been treated for what. Some patients with suspected cancer had their appointments delayed.
Of the latest incident to come to light of delays in the appointments for 442 patients, the trust said matters appear to have been "compounded by the inflexibility of the Care Record Service computer system".
This inflexibility was "combined with the complexity of the trust's clinic structure, which meant that some appointments could not be made during the initial phone call, even though slots were available in specialist clinics".
The trust added, "The issue was also exacerbated by increased pressure on appointment slots arising from the reduction in the maximum waiting time for outpatient appointments."
The trust tackled the delays by increasing capacity in its clinics and by senior clinical staff contacting patients by telephone. Staff also wrote to patients to apologise and to arrange a suitable time and date for their outpatient appointment.
"Specialties likely to have patients with the most urgent clinical need were dealt with first and patients booked in to see a consultant as a matter of urgency. Investigations to date by clinical staff have confirmed that no patient has come to direct clinical harm as a result of this issue."
Julian Nettel, chief executive of Barts and The London NHS Trust, said, "We apologised directly to the patients concerned. We acted as soon as this came to light, but it is clear that we have an underlying issue with our management systems that we are addressing as a matter of urgency to ensure we have the right controls in place."
The total number of GP-referred first outpatient attendances between April and October 2008 was 34,202, and of these 95% were seen within 13 weeks. These patients waited an average of seven weeks from referral to outpatient appointment.
Meanwhile, E-Health Insider has reported that Worthing Hospital may ditch the Cerner Millennium system it bought under the NPfIT.