"We demand the resignation of the key people in the HNS and we appeal to the authorities to stop irregularities and injustice in Croatian football," Torcida spokesman Damir Gruic told state radio.
HNS spokesman Tomislav Pacak told Reuters it had no comment "for now", but may release a statement on Sunday.
The protest was called after Croatia's biggest derby was scrapped last Saturday when visitors Hajduk refused to play against champions and league leaders Dinamo Zagreb after their fans were banned from entering Maksimir Stadium.
Hajduk and their supporters said it was not just those blacklisted as troublemakers who were not allowed into the game in Zagreb and saw the move as further proof of discrimination against their team. Dinamo said they had been provided with the list of troublemakers by police.
They have complained for years that HNS decisions are influenced by Dinamo, putting main rivals Split at a disadvantage.
Hajduk have had to play three home matches this season in an empty stadium as punishment by the HNS for crowd trouble.
Dinamo have won the last nine Croatian league titles.