The two-time gold medallists, who last topped the podium at Athens 2004, won the game with a strong second-half performance after it had been a tight affair in the opening period.
Indeed, the two eastern European sides traded goals for much of the first half, but four Ivan Cupic throws gave Croatia a two-goal advantage at the the hooter as they led 11-9.
But Croatia asserted their dominance after the break and soon established an unassailable six-goal lead, taking a 24-18 advantage into the last five minutes.
That allowed them to see the game out in comfort and book their last-eight spot, with Cupic taking his tally to 23 goals for the tournament while Laszlo Nagy and Gabor Csaszar scored four apiece for Hungary.
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