Bangkok deployed two fighter planes after "an unidentified aircraft crossed into Thailand in Tak province" before disappearing from radar, the Royal Thai Air Force said in a statement.
Thailand has scrambled fighter jets near its border with Myanmar and ordered its defence attache to issue a warning to the military government, its air force says, over what it calls an airspace violation during a combat operation.
Two F-16 fighter jets were deployed when a radar detected a plane in Thai airspace close to the Myanmar border late Thursday morning, air force spokesperson Air Vice Marshal Prapat Sonjaidee said.
"An aircraft from an unknown side violated the border over Phop Phra district in Tak province while attacking ethnic armed group along the border," Prapat said in a statement.
Thailand's air attache in Yangon has been asked to "coordinate with related agencies in Myanmar to send a warning and find preventive measures in the future".
A spokesperson for Myanmar's junta could not immediately be reached for comment.
READ MORE: UN: Over a million displaced in Myanmar
Myanmar's military has stepped up operations against ethnic minority armies since a coup last year and is encountering resistance on multiple fronts, from old enemies to newly formed militia groups allied with the ousted government.
Activists and aid groups have condemned the junta's use of artillery and air strikes in civilian areas. The United Nations humanitarian agency this week estimated nearly 760, 000 people have been displaced by conflict across Myanmar since the coup.
A witness in Thailand told Reuters news agency a fighter jet was seen over two villages about 5 km (3.11 miles) from the border, triggering panic among residents, with one school sending its students to a bomb shelter.
The Thai air force said one of its attaches in Yangon had been instructed to warn relevant agencies in Myanmar and ask them to prevent future infringements.
Thai authorities said close to 300 people have fled an intensification of military operations in Myanmar's Karen state in the past few days.