The police are still establishing if the machine guns, bombs, hand grenades and ammunition were intended for the Croatian or the international market.
Deputy police chief Jakob Bukvic said the types of the weapons seized indicated they were intended for the commission of the gravest crimes, including terrorism.
He added the police had still not established where the weapons came from, but that they were likely from Croatia and Bosnia-Herzegovina, although not accidental "leftovers" from the 1990s wars.
The police have been able to prove that only five of the 13 people arrested were connected with the weapons and the ammunition. They rest were released after being interviewed.
The police confirmed that one of the main suspects was a former Zagreb police officer.
The weapons smuggling ring was cracked after a carefully prepared operation by the Counterintelligence Agency, the Office for the Prevention of Corruption and Organised Crime, and the Police Directorate.
Eleven Croatian citizens aged 25-55 and a 33-year-old Bosnian citizen were arrested on Sunday. Another Croat, also 33, was arrested on Monday. Most were previously known to the police.
The weapons were seized in several flats in Zagreb and one in Bjelovar. In the presence of their attorneys, some of those arrested admitted to the crimes and working together, the police said.
Apart from the five men referred to the Zagreb County Court investigating judge, the police pressed charges against a man for aiding and abetting a crime, and announced charges against a suspect from the Bjelovar area for illegal possession of arms and explosive matter.