Police said on Thursday that the man, identified as Zoran F., had been taken to the Zagreb County Court Remand Centre, while the second suspect, identified as Fran Lj., had not been found.
Both suspects were charged as accessories after the fact.
Matekovic has been sentenced in absence to seven years in prison for his role in the abduction of General Vladimir Zagorec's teenage son.
Police declined to reveal any details of the ongoing investigation.