Last week, Luis Alberto Rubi, Honduras's chief prosecutor, asked the supreme court to issue arrest warrants charging the military commanders.
Those named by the prosecutor included General Romeo Vasquez, the head of the armed forces; General Javier Prince, the air force chief; and General Juan Pablo Rodriguez, the navy commander.
Juan Carlos Sanchez, the defence lawyer for the military commanders, said that there was enough evidence to prove his clients' innocence.
"We will concentrate on showing the facts and they want to face this process to prove the charges are baseless," Sanchez said.
Outside the court, dozens of supporters of Zelaya, who has been staying in the Brazilian embassy in Tegucigalpa since he returned to the country in September, booed the army officers as they went into the meeting with Rivera.
|Supporters of the military commanders have protested against the court decision [Reuters]
A rival group of protesters waved signs of support for the military commanders.
The prosecutor's case does not question whether the coup on June 28 itself was legal, only whether the military went too far in flying him to Costa Rica.
Zelaya was seized by armed soldiers and sent out of the country after the supreme
court and congress ordered his removal over his insistance on going ahead with a referendum that the court had deemed unconstitutional.
Roberto Michiletti, who took over the presidency after Zelaya had been exiled, later acknowledged that sending the president abroad was an mistake and said he should face charges in Honduras.
When the attorney-general called for the charges last week, Zelaya dismissed them as superficial and accused the de facto government of using new tricks.
"... 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.
Porfirio Lobo, the president-elect who will take office on January 27, has said he supports granting amnesty both to Zelaya and to all of those involved in the coup.