Prime Minister Prayut Chan-o-cha warned Thaksin Shinawatra on Thursday to cease making political comments, or the junta would take further action against him.
Gen Prayut said the decision by the Foreign Ministry to revoke Thaksin's two passports was made after his latest public comments.
Thaksin attacked privy councillors in an interview with Chosun Ilbo in Seoul on May 20, saying they were behind the military coup last year.
The coup toppled the interim government of caretaker prime minister Niwatthamrong Boonsongphaisan of the Pheu Thai Party and Gen Prayut, the army commander-in-chief at the time, took control.
Thaksin, who was in the South Korean capital last week for the Asian Leadership Conference, said in the interview on the sidelines of the meeting that his sister Yingluck had been targeted by the coup, to remove her from power, just as he had been in 2006.
She stepped aside shortly before the coup because of court action being taken against her.
Gen Prayut said Thaksin's passports were revoked because he would not stop making political comments.
He indicated that the National Council for Peace and Order has the authority to take more action, but the junta will not use it for now.
The ministry cancelled the passports on Tuesday. They had been issued when Pheu Thai was in power with Surapong Tovichakchaikul as foreign minister.
Mr Surapong said on Wednesday that he would give the passports back to Thaksin if he ever had the chance.
Authorities have been ordered to continue a lese majeste inquiry against Thaksin, the prime minister said.