Hundreds of holiday makers and business people trying to renew their passports were held up as the systems went down.
"There was a failure at 11.58," a Passport Agency spokesman told CW360.com. "All but one office was back up and running by 1.20."
Siemens Business Systems, the Passport Agency's IT outsourcer was investigating the problem, the spokesman said.
Frustrated customers at the Passport Agency's London office told CW360 that staff there had complained of systems problems on Monday.
The Passport Agency and Siemens Business Systems were heavily criticised by the House of Commons Public Accounts Committee after problems with the implementation of a new IT system in 1999 resulted in a backlog of 565,000 passports, delays of up to 50 days and queues outside Passport Agency offices.