The system was brought in to simplify the organisation's pay system but staff, including soldiers on the frontline, have been short changed and forced to pay £30 million back according to a report from the Commons Defence Committee.
The report shows in 2007, 50,764 monthy wage packets were short - some by as much as £350.
A spokeswoman for MoD said: "There were problems with the JPA in the first year of operation. Over the last 12 months, significant improvements have been made to the system and further training has been given to service personnel.
"We apologise for the inconvenience caused by any incorrect payments. We have ensured any repayments were made in a way and at a level that minimises impact upon our people."
