Air Force Space Command last month first acknowledged the issue, which affects the way the ground control system builds and uploads messages transmitted by the GPS IIF satellites, but said it did not affect the accuracy of GPS signals.
At the time, the Air Force said an investigation into the issue had shown the problem had gone unnoticed since 2013.
On Wednesday, the Air Force's GPS Directorate said further data analysis showed that the issue first appeared in 2011, a year after the GPS IIF satellites become operational, and two years earlier than previously thought.
Boeing Co is the prime contractor for the GPS IIF satellites. Lockheed Martin Corp runs the ground system.
The GPS office said the issue was infrequent and only 14 message index errors had been uploaded since May 2010, a tiny fraction of the 80,000 navigation uploads handled by the latest version of the ground system software since October 2007.
It said the GPS ground system was designed to check signals by comparing what was uploaded against what was transmitted, which meant the errors were not initially detected since the signals matched the erroneous upload.
Lockheed has said it has put a "workaround" in place to avoid further errors and is working on a full software correction with the Air Force.
GPS is a space-based worldwide navigation system that provides users with highly accurate data on position, timing and velocity 24 hours a day, in all weather conditions.
The U.S military uses the GPS for targeting precision munitions and steering drones. It also has a wide range of commercial applications for the financial sector, farming and tracking shipments of packages. Car navigation systems and mobile phones use GPS to determine their location.
Boeing recently launched the ninth GPS IIF satellite and expects to complete an on-orbit checkout later this month. The next GPS IIF satellite is due to launch in June.
© Thomson Reuters 2015
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