In March 1990, Ōta retired from the university and in November of the same year was elected governor of Okinawa prefecture on a non-party platform defeating the 12-year sitting governor Junji Nishime. His campaign was based on removing U.S. bases from the island to bring back peace. He also opposed the then proposed bill to provide Japanese troops for United Nations' peacekeeping missions. He had a distinguished record as a governor, outspokenly arguing for the interests of the Okinawan people against both the United States military establishment in the Ryukyu Islands and the Japanese central government. After being elected as governor. Ōta failed to make headway on his campaign promises. His requests to discuss the issue of U.S. military occupation in the prefecture with the U.S. authorities were dismissed, stating that all such discussions would happen with the Japanese central government. In 1991, he reluctantly signed lease agreements that enabled military bases use of private lands. This resulted in disapproval from anti-war masses that had earlier supported Ōta in elections.