The decision was made on Thursday and was announced by the HNS on its website on Friday.
A group of Croatia fans twice interrupted the game at San Siro by throwing flares into the pitch and clashed with the police. They also chanted nationalist slogans.
"The text of the decision suggests that it is a last warning before a truly drastic fine. The HNS condemns hooliganism in the strongest terms possible and once again calls upon all stakeholders in Croatian society to join us in the fight against racism, violence and other unlawful behaviour at football stadiums, because that is in the interest of both Croatian football and society," HNS executive director Damir Vrbanovic said.