The late-night blast at a bus station came after a train was hit earlier this week, although Croatian police have ruled out terrorism.
The explosion at around midnight on Thursday at the Stenjevec local bus station in the western part of the city slightly wounded a man, who was taken to hospital.
Two days before, an explosive device went off under a goods train several hundred metres from the bus station, causing damage but no injuries.
Speaking on Friday at the site of the latest blast, Zagreb’s chief of police Goran Burusic said that he “absolutely excludes terrorism as a motive”.
“All available police forces are working on the case. Last night, policemen with long-barrel guns secured the place,” Burusic said.
He added that he “cannot exclude” the possibility that both incidents were connected.
Police have not yet determined what kind of explosives were used, but said both explosive devices were “amateur made”.
The blasts have caused consternation across Croatia because no such incident has taken place in the country for years.
While the EU accession process has not affected the media’s existential struggle for survival one way or the other, they have made respect for human and minority rights more mainstream.