"North Korea launched, possibly a ballistic missile. We will inform if there are updates," the ministry said in a statement.
An initial statement issued by the Defense Ministry specified that North Korea had "possibly" launched what it believed to be a ballistic missile. Government officials later detailed the projectile flew above Japanese territory towards the Pacific Ocean.
Japan’s Okinawa had issued an air warning, a Sputnik correspondent reported, adding that locals were advised to find shelter in buildings or underground facilities.
"At 04:00 on August 24 (07:00 pm on August 23 GMT), a North Korean missile flew towards the Pacific Ocean," the government said in a statement. "The previously announced call for evacuation is canceled."
Japan has since filed a protest against North Korea for the incident, Chief Cabinet Secretary Hirokazu Matsuno announced.
"The actions of North Korea, including constant missile launches, threaten the peace and security of our country, region and the world community. Such launches, even if they are aimed at launching a satellite, violate UN Security Council resolutions that prohibit North Korea from making launches using ballistic technology," the official told a press conference.
"Despite numerous calls not to launch, this launch is a problem in terms of safety of navigation and life of the population. Japan lodges a strong protest to North Korea and condemns it in the strongest terms."
However, citing military authorities, South Korean media reported it was a "space launch vehicle" that had been the subject of the Wednesday launch.
The latest comes after North Korea earlier revealed it intended to launch a satellite between August 24 and 31, warning Japan that potential debris may result from the operation. It was not specified what the launch entailed, or what type of satellite it planned to dispatch.