General Jaroenchai Hintao insisted the majority of weapons smuggled out of the country do not originate from Thai military stockpiles.
Ethnic rebels along the border with Thailand are reportedly purchasing arms and ammunition on the black market in Thailand.
The Army chief said there were measures in place to oversee and verify the military's arsenal.
"Each time there is concern over arms trafficking activities, investigations have consistently shown that the weapons did not come from [Thai] military forces,” Jaroenchai said.
He also addressed provisions for the expected influx of Myanmar citizens after the junta enforced military conscription for around 14 million young people on Saturday.
Jaroenchai said humanitarian assistance on the border was the responsibility of all sectors. Collaborative efforts were in place in line with Thailand’s policy to set up a humanitarian corridor for displaced Myanmar people on the border, he added.
Meanwhile, border defence forces would continue their task of preventing illegal activities including drug trafficking and arms smuggling, he said.
Emphasising the complexity of the Myanmar border situation, Jaroenchai said the military played a crucial role in maintaining law and order while also ensuring the protection of human rights.