Failures by the Ministry of Defence (MoD) to improve its £245m human resources (HR) system have been criticised by MPs as "unacceptable".

The Joint Personnel Administration (JPA) system was designed to improve and consolidate previously separate systems of payroll, postings, promotions, recruitment and training across the three armed forces. But teething troubles led to many forces personnel being paid incorrectly or not at all, with £29m being paid incorrectly.

And the defence select committee said "uncertainties" over the level of error meant the MoD was having difficulty recovering money paid incorrectly.

Problems were so severe that the National Audit Office was unable to determine the amount of mistakes, forcing it to qualify the MoD's accounts.

Committee chairman James Arbuthnot said the failings are significant because they impact upon several areas critical to satisfaction with life in the services.

"It is, in our view, deeply regrettable that such mistakes were allowed to be made by those charged with oversight of the JPA programme," he said.

"We will continue to monitor the operation of JPA, and hope to find evidence of vastly improved service when we report again next year.”

JPA represented a radical change from the previous system by allowing staff to access and update their own personnel records from around the world.

This contributed to personal data held by the £245m programme being incorrect for up to one in 10 military staff.

And officials who originally conceived the JPA programme - supplied by EDS – placed an insufficient emphasis on financial reporting requirements or the need for management information data from the beginning, the committee report found.

The MoD said last year that self-service satisfaction with the JPA Centre had been as low as 31.5 per cent, although it had recently risen to 45.5 per cent.

Problem with JPA were first revealed by Computing in October 2007, after members of the armed forces posted around the world contacted us to complain about their treatment.