The organisation added all aircraft were accounted for and in voice contact with control towers.
Flights into airports within the Manchester Area Control - north of the Midlands and Scotland - were restricted immediately after the problem emerged at 5.50pm.
The restrictions were partially lifted at 6.30 and a full service is due to resume at 8.15pm.
A spokeswoman said it was unclear how many flights were affected.
She said: “There was a temporary glitch in the radar data processing system.
“We knew where the aircraft were and we were in voice communication throughout.
“As a precaution we restricted the number of aircraft coming into the Manchester area.”
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Portuguese Man of War, from somewhere won't see me until it is too late. (15/03/2010 at 22:51)