Hagino, who won IM bronze in 2012, held the lead following the backstroke and touched home just ahead of Kalisz in a time of four minutes 06.95 seconds.
Kalisz took silver in 4:07.75 and Hagino's team-mate Daiya Seto was third in 4:09.71.
Great Britain's Max Litchfield, 21, in his first Games, was fourth in 4:11.62.
