The family contacted a police station on Saturday evening, saying he had last been seen on December 17.
The police said at a press conference they had launched an investigation, but that at the moment they had no useful information in connection with the case.
Interior Ministry spokesman Zlatko Mehun on Saturday denied a report by "Novo hrvatsko slovo", which alleged that its editor had been arrested and taken to an unknown location and that he had been under constant police surveillance over the past few days.
The police summoned Margetic for an interview about three weeks ago following an order by the Office of the Public Prosecutor, which in turn was prompted by a request from the UN war crimes tribunal in The Hague at the beginning of December that the weekly stop publishing statements and testimonies of protected witnesses, Mehun said.
The spokesman said that Margetic had not responded to the summons, but that the police had taken no action against him since no such order came from the Public Prosecutor.