The Observatory, which relies on a network of sources in Syria, has reported multiple "massacres" in recent days, with women and children among the dead.
The Observatory and activists released footage showing dozens of bodies in civilian clothing piled outside a house, with blood stains nearby and women wailing.
Other videos appeared to show men in military garb shooting people at close range.
AFP could not independently verify the images or accounts.
The leaders of Syria's three main Christian churches as well as the spiritual leader of Syria's Druze minority issued statements calling for an end to the violence.
Aron Lund of the Century International think tank said the violence was "a bad omen".
The new government lacks the tools, incentives and local support base to engage with disgruntled Alawites, he said.