在1941年12月8日日本帝國偷襲珍珠港成功後,帝國日軍隨即開始入侵東南亞,當時佈署在臺灣的九七重轟有第5飛行戰隊、第14飛行戰隊、第62飛行戰隊;在法屬印度支那則有第3飛行戰隊、第12飛行戰隊、第60飛行戰隊、第98飛行戰隊。同日台灣時間早上4點半(日本時間5點半),陸軍第14飛行戰隊所屬之17架九七重轟自臺灣起飛,轟炸呂宋島碧瑤市的海約翰營區(英语:John Hay Air Station),空襲機隊在上午8點19分抵達目標地,毫無損傷的情況下完成任務。隨後九七重轟伴隨帝國陸軍南侵的腳步,提供陸上部隊有效的轟炸支援。由於後繼機百式重爆·吞龍性能平庸,且物資拮据的前線單位對其引擎妥善率不甚滿意,到戰爭中後期九七重轟仍是陸軍的主力攻擊機,直到四式重爆·飛龍服役後帝國陸軍才完成戰術攻擊機的換代。仍服役的九七重轟則轉換為運輸、聯絡、巡邏、拖靶等勤務機運用。
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