Constructed for use during World War II and entering service in 1944, she suffered damage in a friendly fire incident during her maiden voyage which restricted her to use as a training submarine.

[1] On 8 September 1944, she got underway from Inchon and headed south along the west coast of the Korean Peninsula, bound for the main Imperial Japanese Army transport submarine base, located on the Seto Inland Sea at Mishima in Ehime Prefecture on Shikoku in Japan.

[1] Around midnight on 8–9 September, a lookout on the quarterdeck of the Japanese NYK Line 882-gross register ton Type 2E cargo ship SS Izu Maru — an unarmed merchant ship making a voyage from Wakamatsu, Kyushu, Japan, to Dairen, Manchukuo — sighted Yu 3001 at a range of 1,500 meters (1,640 yd).

[1] Izu Maru′s captain, Seinoshin Hiyama, consulted a recognition manual and found that Yu 3001′s silhouette did not match that of any Imperial Japanese Navy submarine.

[1] Izu Maru rammed Yu 3001 on her port side amidships, tearing a large hole in the submarine's No.

[1] The men aboard Yu 3001 escaped serious injury except for an Imperial Japanese Army captain — the navigation officer of the Army Transport Submarine Detachment Headquarters at Inchon, aboard Yu 3001 as a passenger — who suffered painful facial burns when caustic soda hit him.

"[1] Realizing his ship had attacked a Japanese submarine, Hiyama launched Izu Maru′s lifeboat, which rowed to Yu 3001, arriving alongside her 20 minutes after the collision to render assistance.

[1] At Kunsan, the Japanese Army's military police — the Kenpeitai — questioned Hiyama about his collision with Yu 3001 and established the schedule for the following investigation of the incident.