The Justice Department has charged two top Syrian military officials with war crimes committed against Americans and others at a notorious prison in Damascus during the Syrian civil war, according to an indictment unsealed on Monday.

The indictment represents the first time the United States has criminally charged top Syrian officials with a litany of human rights abuses used to silence dissent and spread fear through the country. The whereabouts of the officials, Jamil Hassan and Abdul Salam Mahmoud, are not known, but the indictment clearly signals that the United States aims to hold the former Syrian government officials responsible.

Mr. Hassan and Mr. Mahmoud “sought to terrify, intimidate and repress any opposition, or perceived opposition, to the regime,” according to the indictment, which was filed under seal last month in federal court in Chicago.

The indictment was made public the day after Syrian rebels overthrew Bashar al-Assad, the longtime Syrian leader. Mr. Hassan and Mr. Mahmoud would need to be flown to federal court in Chicago to stand trial, but the charges provide the legal mechanism for American law enforcement to take custody of the men, if they can be found.

Mr. al-Assad has already fled to Russia.

Along with unnamed co-conspirators, Mr. Hassan and Mr. Mahmoud “committed the war crime of knowingly and intentionally conspiring to commit cruel and inhuman treatment,” according to the indictment. The men intended to inflict “serious physical abuse upon victims within their custody or control, namely U.S. citizens and other detainees” held at Mezzeh military air base in the Mezzeh neighborhood of Damascus. Investigators described the location as the Mezzeh prison and said both men had offices at the facility.

Mr. Hassan and Mr. Mahmoud were top leaders under Mr. al-Assad. Mr. Hassan was the head of the Air Force Intelligence Directorate, which oversaw the crackdown on Syrian citizens, and Mr. Mahmoud was a brigadier general in the Air Force Intelligence unit who was in charge of the Mezzeh prison and operations at the military base.