She took part in Battle of Badung Strait on 18–20 February 1942, where she ran aground on one of the channel shores after temporarily losing rudder control.

[8] Haguro would later sink a fellow Dutch warship, the light cruiser HNLMS De Ruyter, with another torpedo hit during the engagement.

[8] Alexander Sharp, the commanding officer, of the nearby United States Navy destroyer USS John D. Edwards, recorded that "Kortenaer, about 700 yards (640 m) bearing 80° relative, was struck on the starboard quarter by a torpedo, blew up, turned over, and sank at once leaving only a jackknifed bow and stern a few feet above the surface."

The Royal Navy destroyer HMS Encounter rescued 113 men from the total of 153, including Lieutenant Commander A. Kroese, and took them to Surabaya.

[9] In 2016, it was discovered that the wrecks of De Ruyter and Java, and much of Kortenaer had disappeared from the seabed, although their imprints on the ocean floor remained.

The Netherlands Defence Ministry suggested that De Ruyter, Java, and Kortenaer may have been illegally salvaged.