The Military Court will still hear some 500 ongoing cases against civilians, a senior junta official said on Tuesday, a day after the regime announced an end to the controversial practice.
Since the 2014 coup, the junta expanded the use of military courts to try more than 1,000 civilians, especially those critical of their rule or the monarchy.
But in a surprise move ahead of a planned visit to the United Nations in New York next week, Prime Minister Prayut Chan-o-cha said military courts would be phased out for civilians.
Rights groups cautiously welcomed the order, which does not cover ongoing cases and offences prior to the announcement.
"The cases that are still under the deliberation of the Military Court will go ahead because they have already entered court procedure," Deputy Prime Minister Wissanu Krea-ngam told reporters.
"There are 1,500 cases in the military courts, of which 1,000 cases have already finished and 500 cases remain," he added.
The military courts tend to have much higher conviction rates and are far harder to appeal.
Some have handed down record jail terms, including a 30-year sentence for a series of Facebook posts by a civilian that were deemed critical of the monarchy.
The new order reflects growing confidence among junta leaders that they have successfully curbed opposition.
"We are confident that the situation is under control," said Deputy Prime Minister Prawit Wongsuwon. "But if (the) situation is out of control we can re-impose this order."
Watana Muangsook, a politician loyal to the ousted government who has been detained by the military several times for criticising their rule, said the order was little more than window dressing.
"If the NCPO is really sincere they should abolish all orders that violate human rights... such as the military's authorisation to arrest, search and detain people without warrants," he wrote on Facebook, using the official acronym for the junta.
The International Commission of Jurists, which has monitored military court trials, said the move was a "welcome step" but called for all pending cases to be transferred to civilian courts.
The new policy will not affect the three southernmost provinces, which have been governed under emergency laws for the past decade as Thai troops struggle to quell a festering Muslim Malay insurgency.
Army officers also still have the power to arrest and temporarily detain civilians nationwide, while Gen Prayut has maintained his right to unilaterally pass any law in the name of national security under Section 44 of the 2014 interim charter.
According to the Thai Lawyers for Human Rights data, the Military Court handled 1,546 cases involving 1,811 civilians from May 22, 2014 to Sept 30, 2015 in the provinces and to May 31, 2016 in Bangkok.
Source: Thai Lawyers for Human Rights