The National Economic and Social Development Board (NESDB) will study the proposal, which could take 300 days, Interior Minister Charupong Ruangsuwan said after a meeting of the panel on special economic zone policy on Wednesday.
The NESDB would send its conclusions to the ministry, he said.
Mae Sot district in Tak and Mae Sai district in Chiang Rai have been picked by the committee chaired by Prime Minister Yingluck Shinawatra.
The prime minister met Gen Min Aung Hlain, commander-in-chief of the Myanmar Armed Forces, on Tuesday and discussed the importance of border trade between the two countries and its potential to play a key role in trade ties between Thailand and Myanmar.
Mae Sot and Mae Sai are major trading posts between Thailand and Myanmar. Two-way trade between Mae Sot and Myawaddy totalled 250 billion baht in the first half of this year. Trade with Myanmar through Mae Sai totalled 6.8 billion baht during the same period, according to Commerce Ministry figures.
Most Thai exports through Mae Sot were destined for Yangon, but some products via Mae Sai were sent to southern China through northeastern Myanmar.
Mr Charupong said it was necessary to consult the Myanmar government on the plan, especially rules and regulations to benefit investors in the zones.
The special economic zone would offer tax and other incentives to attract factories.
The Thailand Development Research Institute has already supported the setting up of special economic zones in both locations, and also in Sangkhla Buri in Kanchanaburi, at Mukdahan, opposite Laos, and in Aranyaprathet district of Sa Kaeo opposite Cambodia.