An army spokesman told local radio that Vasquez had called on military lawyers to take on the case.
Zelaya, who has been holed up in the Brazilian embassy since returning to Honduras in September, immediately dismissed the charges as superficial and accused the de facto government of using new tricks.
"Today, using a new stratagem, the attorney-general who has equal or more responsibility as the soldiers, is presenting accusations ... to achieve impunity for the soldiers by accusing them of minor crimes," Zelaya said in a statement.
The Honduran congress is set to to debate an amnesty for those involved in the coup, which could be approved next week.
Roberto Micheletti, the country's de facto leader, said on Wednesday he would step down on January 27, when conservative Porfirio Lobo, who who won controversial November presidential elections, is due to take office.
Micheletti also said, in a television interview cited by the Honduran national media, that the US had offered "millions of dollars in aid" to the country if he would step down.
The US along with the European Union and international organisations, froze millions of dollars of much-needed aid to Honduras after the coup.
Many critics of the Micheletti's military-backed government, particularly in Latin America, said November's poll were an endorsement to the coup in a region with a painful history of dictatorships.
They have sought for Zelaya to return to office to finish his term as a possible solution to the crisis.