Excavation teams were reported to be still working at the site on the Nabi Azir hilltop position formerly occupied by Syrian soldiers.
Residents from the nearly town of Anjar claimed at least one of the bodies recovered was dressed in a Lebanese soldier's uniform.
Officials said remains had been taken away for DNA testing.
The Anjar headquarters was notorious for the arrest and torture of prisoners during nearly 30 years of Syrian military presence in Lebanon.
Dozens of Lebanese were reported to have disappeared during this period.
Another 24 bodies were found last month in a mass grave near the Lebanese military of defence near the capital, Beirut.
It was thought the bodies were those of Lebanese soldiers killed during a Syrian military offensive in October 1990.