The 27-year-old man was arrested in a refugee shelter in western Austria in June after being denounced by a fellow Syrian.
At first he admitted to the 2013-2014 killings in Homs and the surrounding region but later retracted his confession, a spokesman for public prosecutors in the Austrian city of Innsbruck told AFP.
The suspect, a member of a unit of the Free Syrian Army (FSA), faces life in prison if convicted. He will go on trial early next year.
The prosecutors were able to bring charges against the man under an international counterterrorism agreement, which is intended to prevent political murders from remaining unpunished if a criminal flees abroad.