The NHS Information Authority and the national programme for IT suffered a "major hardware failure" that caused "server disruption in communications" in September.
The organisations are responsible for the government's £2.3bn investment in NHS IT.
The failure was revealed in NHSIA board minutes published last week. The disruption took place on 1 and 2 September, and affected 600 staff working for the NHSIA and the national programme for IT.
A spokeswoman for the NHSIA said the majority of incoming e-mails received during this time were fully recovered.
"A proportion of NHSIA and national programme for IT staff have alternative e-mail facilities so the impact, although serious, was not catastrophic," she said.
The incident occurred following a single hard disc failure on one of the NHSIA's two Exchange servers, which was followed by failures in a second hard disc, motherboard SCSI card, a SCSI cable and a tape back-up drive.
The NHSIA has since added two back-up servers as a safeguard against future disruption to its e-mail system.
The back-up servers were put in place following recommendations by consultancy the NCCGroup.