"The launch is a clear violation of UN Security Council resolutions, and poses a threat in terms of security," the ministry said in a statement, quoted by the Kyodo news agency.
The protest was transmitted through diplomatic channels through the Japanese Embassy in China, the agency said.
Japanese Prime Minister Shinzo Abe called the launch a grave threat to Japan security and an "unforgivable act," and ordered ministries to prepare for emergencies to ensure the safety of the population, as well as to start collecting and analyzing the information on the issue.
US and South Korea began Monday the Ulchi-Freedom Guardian large-scale military exercise, the computerized command and control implementation, which mainly focuses on defending South Korea from a possible North Korean attack.
Pyongyang has repeatedly claimed that the joint military drills are a rehearsal for a real attack on North Korea. The United States and South Korea, in their turn, insisted that the exercises are aimed at training defensive skills for combating emerging threat from the North.