Gen Min Aung Hlaing said he had confidence in the Thai armed forces as "they are duty-bound to maintain national security and ensure safety for the public", the Supreme Command quoted him as saying in a press release on his talks with Supreme Commander Gen Tanasak Patimaprakorn.
"We also have confidence in the success of the National Council for Peace and Order (NCPO) roadmap," he added, according to the press release.
Myanmar went through a worse situation than Thailand in 1988, he said.
He was referring to the crackdown by his country's armed forces on pro-democracy demonstrators in 1988 and subsequent rtejection of the results of the 1990 election won by Aung San Suu Kyi's National League for Democracy.
During their talks, the two generals discussed issues of mutual concern including migrant labour.
Gen Tanasak, who is the NCPO deputy chairman, said all Myanmar workers in Thailand would be well taken care of, according to the press release. The junta has begun carrying out a plan to end the use of illegal migrants and legalise their status in Thailand.
He pledged deepening cooperation with Myanmar at all levels including defence relations, strengthening border ties, an exchange of military personnel and the participation of Myanmar in the joint Cobra Gold military drills this year.
The coup regime set up the first centre to register illegal workers from Myanmar, Laos and Cambodia in Samut Sakhon province on Monday. Similar one-stop centres are due to be opened in all provinces by mid-July as part of the policy to end the illegal, lucrative business of trafficking in illegal, smuggled labour.
Thailand has an estimated 2.2 million foreign workers, most of them from Myanmar and Cambodia. The Thailand Development Research Institute estimated another 900,000 illegal workers are in the country.