The NHS's new data spine, a backbone of the national programme for IT (NPfIT), was down for 1,680 minutes, or 28 hours, in the week ending 1 January.
Doctors and IT staff said there were continuing difficulties logging into national systems through the spine.
The data spine is described by Connecting for Health, which runs the NPfIT, as a core building block of the NHS Care Records Service. The service is being designed to hold records on 50 million patients. It is also used as part of the electronic version of Choose and Book, which allows patients and doctors to pre-book hospital appointments online.
Doctors' representatives said the downtime would add to the concerns of clinicians about the performance of new national systems, and to what extent they will wish to rely on centralised and regional equipment. The latest outages are said by some doctors to have left them unable to carry out their normal work.
Connecting for Health said there were "ongoing problems around the Spine Patient Demographics Service [PDS]". This contains details of a patient's NHS number, name, address and date of birth. The problems are "resulting in users experiencing periods of downtime or very slow performance".
The spine holds demographic information and summarised clinical information such as allergies, emergency hospital visits and adverse reactions to drugs. It is also used to provide an interface between local and NPfIT systems. It is run by BT.
Connecting for Health said the problems were also affecting other services, including those offered by local service providers that are "spine-enabled".
"Details about the service downtime and response times are being clarified with BT Spine [the contractor]," said Connecting for Health.
Despite the 28 hours outage, Connecting for Health has reported on its website that the overall level of spine availability for the week ending 1 January was 95.8%.
"The availability/downtime figures here are currently the most accurate assessment possible and do not reflect the severely degraded response times experienced by users," it said.
In a statement, the organisation said, "NHS Connecting for Health can confirm that some of the NHS organisations using our systems and services have been experiencing some intermittent interruptions with one part of the spine service, with slow response times when accessing PDS.
"NHS Connecting for Health is working together with suppliers to address the issues which have surfaced, and by yesterday [5 January] a near normal service has been operating."