The order, signed by CAAT chairman Suttipong Kongpool, also covers eating and drinking of food or beverages brought by passengers.
The decision came after a new wave was reported in Bangkok earlier this month, which quickly spread to several provinces nationwide.
The ban will be in effect until the situation improves or a new regulation is announced.
The CAAT also has prohibited the distribution of newspapers, magazines or any pamphlets to passengers on flights, except those related to safety, in order to minimise passengers touching surfaces that could spread the virus. Selling of souvenirs or duty-free goods in-flight is also prohibited.
Other measures that airlines need to follow include installing infrared thermal scanners for passengers and staff, enforcing the wearing of face mask at all times on board except in emergency cases, and following social distancing.
For flights that are longer than 90 minutes, the airline must reserve the last two rows of seats at the back to quarantine passengers suspected of being infected.