More than 50 people were killed in the attack on Thursday on a police training school in the coastal city of Zliten, a security source said, in the deadliest single attack in Libya since the fall of Moamer Kadhafi.
The 15-member council described the suicide bombing as a "heinous act" and said those responsible should be brought to justice.
It also condemned a separate attack the same day on a checkpoint in Ras Lanouf, home to a key oil terminal, in which six people died including a baby.
The United Nations brokered the unity government deal that was signed by politicians last month, but the agreement does not have the full backing of Libya's rival parliaments.
Libya has had rival administrations since August 2014, when an Islamist-backed militia alliance overran Tripoli, forcing the government to take refuge in the east.
EU foreign affairs chief Federica Mogherini yesterday met in Tunis with the prime minister-designate of the new unity government, Fayez al-Sarraj, and unveiled a 100-million-euro aid package.