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 to account those who were at the highest echelons of the Syrian government.

Mr. Hassan, who was the head of the Air Force Intelligence Directorate, and Mr. Mahmoud, a brigadier general in the Air Force’s intelligence unit, “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 the government of President Bashar al-Assad of Syria. 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, an authoritarian leader known for his brutal tactics during a 13-year civil war, has already fled to Russia, which, along with Iran, had helped keep him in power.

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