Ōta also had experience with the Japanese Special Naval Landing Forces (SNLF, the Japanese equivalent of the Royal Marines), having been assigned as battalion commander to Japanese SNLF forces in the 1932 First Shanghai Incident. He was promoted to commander in 1934. In 1936, he was named executive officer of the battleship Yamashiro, and was finally given his first command, that of the oiler Tsurumi in 1937. He was promoted to captain in December the same year.

In 1938, with the start of the Second Sino - Japanese War, Ōta was assigned to command the Kure 6th SNLF. In 1941, he was assigned to the command the SNLF under the Japanese China Area Fleet at Wuhan in China. He returned to Japan the following year, and was assigned to command the 2nd Combined Special Naval Landing Force that was earmarked for the seizure of Midway in the event of a Japanese victory over the United States Navy at the Battle of Midway. Although this never came to pass, he was promoted to rear admiral and commanded the 8th Combined Special Naval Landing Force at New Georgia against the American First Raider Battalion. He then served in various administrative capacities until January 1945, when he was reassigned to Okinawa to command the Japanese Navy's forces as part of the Japanese reinforcement effort prior to the anticipated invasion by Allied forces.

In Okinawa, Ōta commanded a force with a nominal strength of 10,000 men. However, half were civilian laborers conscripted into service with minimal training, and the remainder were gunners from various naval vessels with little experience in fighting on land. Allied sources are contradictory on his role as commander of the naval elements in Okinawa. Some cite Ōta as able to organize and lead them into an effective force, which fought aggressively against the Allied forces, "withdrawing slowly back to the fortified Oroku Peninsula." But Naval elements, except for outlying islands were headquartered on the Oroku peninsula from the beginning of the battle. Operations Planning Colonel Hiromichi Yahara of the Japanese 32nd Army describes a miscommunication occurring in the order for Ota's Naval elements to withdraw from the Oroku Peninsula to support the army further south. What did happen is clear: Ota began preparations on or around May 24, for the withdrawal of all Naval elements to the south in support of the Army. He destroyed most all heavy equipment, stocks of ammunition and even personal weapons. While in mid march the south Japanese 32rd Army HQ ordered Ota back into the Oroku peninsula citing that a mistake had been made in timing (explanations vary). Naval elements returned to their former positions with no heavy weapons and with about half the troops with no rifles. The Americans, who had not noticed the initial withdrawal attacked and cut off the peninsula by attacks from the north on land, and one last seaborne landing behind the Navy's positions. Naval elements, then committed suicide with whatever weapons possible, with some leading a last charge out of the cave entrances. According to the Japanese museum for the Japanese underground Naval Headquarters in Okinawa, "4000 soldiers committed suicide" inside the command bunker including Ota.

On 11 June 1945, the U.S. 6th Marine Division encircled Ōta’s positions, and Ōta sent a farewell telegram to the IJA 32nd Army Headquarters at 16:00 on 12 June (although the Naval Headquarters Museum in Okinawa, posts in a translation that the last telegram was sent at 20:16 hours, on 6 June 1945). On 13 June, Ōta committed seppuku -- ritual suicide for failing to defend Okinawa, Japan. He was posthumously promoted to vice admiral.

Sent at 20:16 on the 6th of June, 1945: "Please convey the following telegram to the Vice - Admiral. While the Governor should be the person to relay this report on the present condition of the Okinawa prefectural inhabitants, he has no available means of communication and the 32nd Division Headquarters appears to be thoroughly occupied with their own correspondences. However, due to the critical situations we are in, I feel compelled to make this urgent report though it is without the Governor's consent. Since the enemy attack began, our Army and Navy has been fighting defensive battles and have not been able to tend to the people of the Prefecture. Consequently, due to our negligence, these innocent people have lost their homes and property to enemy assault. Every man has been conscribed to partake in the defense, while women, children and elders are forced into hiding in the small underground shelters which are not tactically important or are exposed to shelling, air raids or the harsh elements of nature. Moreover, girls have devoted themselves to nursing and cooking for the soldiers and have gone as far as to volunteer in carrying ammunition, or join in attacking the enemy. This leaves the village people vulnerable to enemy attacks where they will surely be killed. In desperation, some parents have asked the military to protect their daughters against rape by the enemy, prepared that they may never see them again.

Nurses, with wounded soldiers, wander aimlessly because the medical team had moved and left them behind. The military has changed its operation, ordering people to move to far residential areas, however, those without means of transportation trudge along on foot in the dark and rain, all the while looking for food to stay alive. Ever since our Army and Navy occupied Okinawa, the inhabitants of the Prefecture have been forced into military service and hard labor, while sacrificing everything they own as well as the lives of their loved ones. They have served with loyalty. Now we are nearing the end of the battle, but they will go unrecognized, unrewarded. Seeing this, I feel deeply depressed and lament a loss of words for them. Every tree, every plant life is gone.

Even the weeds are burnt. By the end of June, there will be no more food. This is how the Okinawan people have fought the war. And for this reason, I ask that you give the Okinawan people special consideration, this day forward".