NHS England has been granted temporary permission to use sensitive patient information, after being forced to make an urgent application for a special legal exemption, HSJ has learned.

The organisation requested the exemption to enable it to handle patient identifiable data, after discovering that permissions that applied to the old commissioning system were not transferring to the new one.

This meant that for the first week after the NHS reforms took effect, NHS England, clinical commissioning groups and commissioning support units were unable to handle patient identifiable data from the “secondary uses service” for purposes other than the direct commissioning of patient care.

That meant, for example, NHS England and the 19 CSUs it hosted could not process information containing patients’ NHS numbers in order to analyse health outcomes for patients with a particular condition.

The restriction also prevented NHS England, CSUs and clinical commissioning groups from analysing patient identifiable data for the purposes of gaining insight into population health, monitoring provider performance, or developing national guidelines.

NHS England, previously known as the NHS Commissioning Board, applied to the NHS Ethics and Confidentiality Committee for a legal exemption under section 251 of the 2006 Health and Social Care Act. The exemption would set aside normal confidentiality requirements where there is no practical alternative, and where it is in the public interest to do so.

However, the exemption has not been approved. Instead, the NHS Health Research Authority, which took over responsibility for such decisions at the beginning of April, has given “conditional approval”.

In effect, it extends the permissions that existed for the Department of Health, primary care trusts and strategic health authorities to the new structure for three months.

HSJ understands this is viewed as a compromise, and is not what NHS England asked for. The body is understood to be dramatically extending its data analytics capabilities, and had applied for permissions that would enable it to do more analysis of patient data than the old system had done.

The Health Research Authority will consider the issue at a meeting on April 18 and April 19. However it is not certain that the matter will be resolved at that point.

A Health Research Authority said: “An interim application was considered by the Health Research Authority’s confidentiality advisory group and approved by the secretary of state on 5 April for a three month period.

“This permits secondary uses service data flows for clinical commissioning groups and commissioning support units for commissioning purposes.

“The full application, with additional data flows, will be considered by the first meeting of the confidentiality advisory group on 18 and 19 April 2013.”