He said that some Patriots have been kept on high alert for years, while between 50 to 70 of them are swapped around each year for tests.
Officials said it was impossible to predict how long it would take to find the cause of the problem.
Lieutenant General Paul Kern said the hundreds of Patriot missiles stationed in the Gulf and South Korea were affected and said the missiles were swapped 10 days ago.
The US warned seven other countries about possible technical problems last week.
The countries are Israel, Saudi Arabia, Kuwait, the Netherlands, Germany, Japan and Taiwan.
Asked why they had not been informed earlier of the problem, General Kern said: "We did what we thought was a very fair assessment of keeping the security of our forces and or allies in check, and we think we did it the right way."
Left on high alert
General Kern said the glitch might have been caused by leaving the missiles on "hot status" alert for more than six months at a time.
Tests have shown that missiles kept constantly on high alert have developed problems in receiving a radio frequency downlink, which guides the missiles in flight.
General Kern said the Patriot's manufacturer, Raytheon Co., had guaranteed that the missiles would work properly if on high alert for a maximum of six months.
He said that some Patriots have been kept on high alert for years, while between 50 to 70 of them are swapped around each year for tests.
Missiles that developed problems have been in operation for between three and 10 years.
Repair costs are estimated at between $80,000 and $100,000.
The Patriot became famous during the Gulf War in 1991 when it was used to shoot down Iraqi Scud missiles in flight.