More than 4,500 passengers are affected due to the disruption at Frankfurt, Germany's largest airport.
By noon, 66 flights had been cancelled, reported AFP, according to the air navigation service agency Deutsche Flugsicherung DFS, which cited an IT glitch in its control centre in Langen.
Passengers have been advised to look for information on their flight before travelling to the airport.
The software malfunction was detected by DFS at its centre in Langen in the central state of Hesse. The glitch has been affecting air traffic over large parts of the country since Wednesday last week.
It has reportedly caused problems in the German airports of Frankfurt am Main, Cologne/Bonn, Stuttgart and Dusseldorf. Airline safety, however, is not impacted, DFS confirmed.
The affected software provides air traffic controllers with 'control strips' of data about the progress of a flight.
The DFS said this system was not functioning properly so they had decided to reduce the volume of traffic in their airspace so that they could monitor all flights more closely. Technicians plan to install alternative software later this week.
The Langen centre monitors an airspace stretching from Lake Constance in the south to Kassel in the north. In the west, the Langen airspace stretches to the French border and in the east to Thuringia.
All other air traffic control systems are fully available and other control centres run by the DFS in Munich, Bremen and Karlruhe, are not affected by the disruption.
Around 2,000 air traffic controllers manage up to 10,000 flights a day in German airspace, which adds up to more than three million a year.