The men, 56-year-old Anwar R. and Eyad A., 42, were arrested on Tuesday in Berlin and Rhineland-Palatinate state. Both left Syria in 2012.
Also Tuesday, another Syrian believed to have worked for the secret service was arrested in France in what was a “coordinated” operation, the federal prosecution in Karlsruhe said.
“From April 2011 at the latest, the Syrian regime started to suppress with brutal force all anti-government activities of the opposition nationwide,” a prosecution statement said.
“The Syrian secret services played an essential role in this. The aim was to use the intelligence services to stop the protest movement as early as possible.”
Anwar R. had allegedly led a secret service division that operated a prison in the Damascus area, and had participated in the torture and abuse of prisoners from April 2011 to September 2012.
“As head of the investigative department, Anwar R. directed and commanded prison operations, including the use of systematic and brutal torture,” it said.
Eyad A., a former officer who had manned checkpoints and hunted protesters, had allegedly aided and abetted two killings and the physical abuse of some 2,000 people between July 2011 and January 2012.
In the summer of 2011, he manned a checkpoint near Damascus where around 100 people per day were arrested then jailed and tortured in the prison headed by Anwar R.
Several other cases pending
The conflict in Syria has killed more than 360,000 people and displaced millions since it began in 2011 with the brutal repression of anti-government protests.
Several other legal cases are now pending in Germany against the regime of President Bashar al-Assad.
Last year, German prosecutors issued an international arrest warrant for Jamil Hassan, a top Syrian official who headed the notorious airforce intelligence directorate and is accused of overseeing the torture and murder of hundreds of detainees.
Although the alleged abuses did not happen in Germany, the case has been filed under the legal principle of universal jurisdiction, which allows any country to pursue perpetrators regardless of where the crime was committed.
The Berlin-based European Center for Constitutional and Human Rights has also joined with torture survivors to file criminal complaints against 10 high-ranking Syrian officials, accusing them of crimes against humanity and war crimes.