More than 12,500 servicemen and women were underpaid between January and September last year as a result of continuing glitches in the Ministry of Defence's problem-plagued computerised salary system.

The biggest fault with the Joint Personnel Administration network affected travel allowances for more than 10,700 part-time reservists, according to figures obtained in a parliamentary written answer.

They had to wait four months to be credited with the money they were due for using their own transport to report for duty at drill halls or bases.

Another 666 people who had been promoted had to wait a month for unit clerks to update their records manually after the JPA computer failed to recognise the changes in rank or alter pay grades.

Manual changes had also to be made in the £126.4m system so that 54 reserve pilots, navigators and observers could receive their pay. A further 90 servicewomen were underpaid by four days salary a month when the computer miscalculated maternity pay.

The MoD said that initial problems with JPA, which caused havoc with RAF salaries and allowances when it was first introduced in 2006, were being ironed out.

"Between January and September last year, 1.83 million basic payments were made without a hitch. Problems are addressed and fixed as we encounter them," a spokesman said. "That is reflected in the relatively minor nature of any complaints compared to two years ago."

When the system was introduced, the MoD was inundated with complaints of under or over-payment, double-charging for married quarters rental and non- payment of flying allowances for aircrew.

An RAF source said yesterday: "There were problems when the system was manual and staffed by clerks working on paper. There are problems now, but fewer of them."

The JPA contract was handled by EDS, the Texas-based firm which operated the equally problem-ridden Child Support Agency, Inland Revenue and Pension Credit computer systems.

All pay and personnel issues for the forces are dealt with by staff at the MoD's Kentigern House, Glasgow.