The Department of Transportation says all lights affected by the issue are now working properly again.
Motorists began reporting that many lights were not operating correctly and flashing yellow and red only.
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The 311 system was flooded with calls about the issue in all five boroughs. The calls were relayed to police to respond in order to prevent accidents.
Drivers and pedestrians were advised to use extreme caution.
The city Department of Transportation says a routine software upgrade experienced an interruption which affected multiple intersections citywide, causing the flashing.
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No accidents were reported as a result of the problems. Police officers were stationed at the affected intersections to direct traffic.
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