Armed forces chief of staff Gen Romeo Vasquez is among those charged
Honduran prosecutors have charged three military chiefs with abuse of power in connection with the ousting and exile of President Manuel Zelaya last June.
The Supreme Court will now decide whether to start a case against them.
Mr Zelaya was removed from office amid a row with the courts, Congress and the military over his plans to look at rewriting the constitution.
He was flown out of the country but returned in secret last September and remains holed up in Brazil's embassy.
The attorney general's office has issued charges against the military high command - the armed forces chief of staff, General Romeo Vasquez, and five others.
A spokesman said they were being charged with abuse of authority for sending Mr Zelaya out of the country. Under the Honduran constitution, it is illegal to forcibly remove Honduran citizens from the country.
"We will submit ourselves to Honduran justice if necessary because we are men of the law," Gen Vasquez told local media.
Mr Zelaya dismissed the charges as a cover to obscure the truth of what happened on 28 June.
"If they are saying that the armed forces committed an error, then that error is called a coup, and the error was subsequently ratified, or rather confirmed by the National Congress," he said.
The reasons for and manner of Mr Zelaya's ousting have been bitterly disputed.
The Supreme Court ruled that his plans to look at changing the constitution were in themselves a violation of the constitution and ordered his arrest, while Congress voted to remove him from office.
However, instead of being detained and charged in Honduras, Mr Zelaya was seized by soldiers who burst into his home and driven to the airport. There he was put on a flight to Costa Rica.
The speaker of Congress, Roberto Micheletti, constitutionally second-in-line to the presidency, was sworn in as interim leader.
Mr Micheletti's government and the military have insisted his removal was a constitutional transfer of power. Many regional countries, the UN, the Organization of American States (OAS) and the European Union condemned the situation as a coup and demanded Mr Zelaya's immediate reinstatement.
However, Mr Zelaya's chances of returning to office to serve out his term appear slim.
In November, a presidential election was held as scheduled and the man elected, Porfirio Lobo, is due to be sworn in on 27 January.
Congress is next week set to begin debating an amnesty both for Mr Zelaya and all those involved in the events in June.