Aerothai vice-president Thinnakorn Chuwong said the new air traffic control system was used for the first time in Bangkok's Suvarnabhumi and Don Muang airport.
He admitted its use caused delays to flights, both in and out, of up to 1 hour 45 minutes at Suvarnabhumi and 1 hour 30 minutes at Don Mueang.
He said 130 flight were affected in total.
State-owned Aerothai, the air navigation service provider, had fixed the problem by noon, reports said.
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After that, there would be no more flight delays, Thinnakorn said.
Thinnakorn said it was neccessary to adjust the timing for flight depatures and arrivals from two minutes per flight to 4 minutes per flight.
As the timing was adjusted, the delays built up.