The Ministry of Defence (MoD) has admitted that more work is required to the troubled £245m Joint Personnel Administration (JPA) programme unifying pay and administration for all three armed forces.

A briefing for MPs on the Commons Defence Committee revealed improvements are needed to provide better management information, prevent fraud, save on back-office functions and reduce costs. The report also revealed the army remains desperately short of information systems engineers.

But the MoD claimed that problems that lead to a total of 78,000 overpayments and 20,000 underpayments to soldiers, sailors and airmen and women have been largely cleared up and the EDS-supplied JPA system is stable and "fit for purpose" with payroll accuracy "consistently in excess of 99 per cent".

“There are now no known IT issues of any significance,” said the briefing.

The MoD blamed incorrect input, the need for a change in culture among users, and lack of training for some of the teething problems.

A breakdown of some of the consequences showed 2,600 overpayments "due to the double-payment of the female clothing grant", with some underpayments due to late payments of bounties, travel claims and allowances or the use of an incorrect rank.

Computing revealed last October that problems with JPA were seriously affecting morale in the armed forces.

We received more than 150 separate complaints from service personnel, including those seeing action in Iraq and Afghanistan, facing continuing financial issues because of JPA.