A 12-year-old girl was killed in Petrinja and five people died in the town of Glina, Croatian officials said, adding that a total of 27 people were injured.
Rescue workers are scouring the rubble of damaged buildings in the search for survivors.
Many people, who were too afraid to return to their homes overnight in case aftershocks caused more damage, slept in their cars or stayed with relatives in other areas.
The earthquake was followed by numerous aftershocks, the strongest of which with a magnitude of 5.0.
It was the strongest earthquake in Zagreb since the 1880 earthquake and caused substantial damage in the historical city center.
Over 1,900 buildings are reported to have become uninhabitable by the earthquake damage. The earthquake was also felt in Slovenia. (ILKHA)