"Hajduk are suspended due to unpaid obligations towards FC Sibenik, while the other two clubs have unpaid obligations towards their players," HNS said on its website.
It was not immediately clear how long the suspensions would remain in force and the HNS was not available for further comment.
Hajduk are second in the league, 13 points behind Dinamo Zagreb, while Sibenik and Karlovac are in the relegation zone.
Several Croatian clubs have been plagued for months with severe financial difficulties.
The anti-graft police (USKOK) recently arrested several people, including some HNS officials, on suspicion of taking bribes to fix matches.
Science and Sports Minister Zeljko Jovanovic, who took office in December, has blamed the HNS for the poor state of the game and called for changes in the body's leadership.
Last week UEFA promised to stamp out abuse of professional players in Eastern Europe, saying they were subject to threats, violence and non-payment of salaries.
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