Croatia's anti-corruption agency USKOK said it is investigating Zdravko, the president, and Zoran, the coach of Dinamo Zagreb, the dominant club in Croatia, over tax fraud and bribery - worth about 200 million kuna ($A39 million).
They were held on Saturday on entry to Croatia from Slovenia, where Dinamo was in training camp, Croatian media reported.
Croatian football federation executive director Damir Vrbanovic was also detained, and so was a tax inspector suspected of helping the suspects defraud the tax authorities.
The operation began on USKOK's orders on Thursday with a raid on the Mamics' homes.
Zdravko Mamic, 55, has frequently been in the media focus over allegations of manipulation and verbal, often vulgar, clashes with critics, including reporters.
The less exposed Zoran, 43, is a former Croatian international who played for Dinamo, Bundesliga clubs Bochum and Bayer Leverkusen, and other German clubs.
The brothers are believed to wield huge influence over domestic football, including the promotion and transfer of players nationally and internationally.