Complaints to the Glasgow (Scotland) Herald were of both underpayment, overpayment and non-payment.
"I live in an unfurnished married quarter," one RAF member told the newspaper. "But I'm being charged for two fully furnished quarters and for living in the mess and full food contributions when I eat at home. I have complained endlessly to no effect."
The automated system was set up and is operated by EDS, the U.S. company founded by H. Ross Perot. EDS has set up a number of computerized systems in Britain.
The Ministry of Defense has acknowledged it has received at least 8,000 complaints since April. But officials say most have been resolved.