Prime Minister Prayuth Chan-ocha and head of the junta passed the order published in the Royal Gazette on Monday night with its immediate effect.
However, the order does not apply to the current open cases, EFE news reported.
The use of military courts was one of the first measures adopted by the junta shortly after seizing power in a coup in May 2014.
The military government tried all cases, including those they considered a threat to national security or in disobedience of its orders and illegal possession of weapons, in these courts.
According to Thai lawyers, at least 1,811 civilians were prosecuted in military courts since the coup, denouncing the lack of legal guarantees provided in these courts, including refusing the right to appeal or bail.
The junta justified the decision to return all civil cases to the ordinary courts for the betterment of the situation, following the approval of a new Constitution in a referendum in August, which strengthens the military hegemony in the country's politics.
In the last two years peace and has been restored with people cooperating well to move the country towards sustainable development, reform and a fair reconciliation, stated the order.
The decision, which retains the ability of the military to perform police duties - including the detention of suspects up to seven days in barracks - was described as a "limited step" by Human Rights Watch (HRW).
HRW condemned the measure as being "the military junta's way of deflecting criticisms by the UN Human Rights Council" which meets on Tuesday in Geneva.
