The armed forces’ £100m Joint Personnel Administration (JPA) programme has failed to meet four of the seven key targets set for the scheme this year, including those on pay accuracy, timeliness of payments and cost reductions ­ decreasing planned savings by around £5m.

JPA, which is supplied by EDS, was intended to overhaul the way the armed forces are paid, harmonising pay systems across the forces and giving employees control over their own information.

But organisational upheaval and operational problems led to the missed targets, according to Trevor Spires, chief executive of the Service Personnel and Veterans Agency (SPVA), which runs the system.

“Inevitably, against a background of high operational tempo for the armed forces, JPA implementation and the formation of the new agency, there have been some challenges in achieving the required standard of performance,” he said in the SPVA annual report.

SPVA and EDS have always maintained that the programme has been broadly successful, saving £100m and cutting HR staff numbers by 20 per cent.

But Computing continues to receive complaints from service personnel unhappy with the system.

One Royal Marines HR administrator, who did not want to be named, said JPA is still beset with problems.

“In the last month [September] every time someone is reverted from a local or acting rank they have been put back to the lowest increment level of their proper rank. In some instances this has meant that a lance corporal who has been serving for six years is reverted and somehow put onto a recruit’s wage,” he said.

An SPVA spokesman said: “Missing the targets was the result of organisational change rather than problems with the technology.”