Several injuries reported as well as considerable damage to buildings in Petrinja, a town southeast of the capital, according to Al-Jazeera.
The earthquake was felt throughout the country on Tuesday, as well as in neighboring Serbia, Bosnia and Herzegovina, and as far away as Graz in southern Austria.
Buildings collapsed in Petrinja, some 60km (37 miles) from Zagreb.
An Al Jazeera reporter in the town witnessed a boy and his father being pulled from a car buried in the rubble.
The European Mediterranean Seismological Center said the 6.3 magnitude earthquake hit 46km (17 miles) southeast of Zagreb.
The same area was struck by a 5.2 quake on Monday.
Croatian Red Cross said it was responding to a “very serious” situation in Petrinja following the earthquake.
Croatian media said people were injured by the quake, but could not initially say how many amid the confusion and downed phone lines.
Croatian seismologist Kresimir Kuk described the earthquake as “extremely strong”, far stronger than another one that hit Zagreb and nearby areas in spring.
He warned people to keep out of potentially shaky, old buildings and move to the newer areas of the city because of the aftershocks.
MNA/PR