Earlier in the day, South Korea's Yonhap news agency reported about the launch of two ballistic missiles from the North Korean province of North Pyongan toward the Sea of Japan. The missiles did not reach the Japanese exclusive economic zone.
The projectiles flew 410 kilometres, reaching a 50-kilometre height, the South Korean Joint Chiefs of Staff (JCS) said.
According to the NHK broadcaster, the protest was voiced over the fact that the missiles had been launched in violation of resolutions of the UN Security Council.
Japanese Prime Minister Shinzo Abe ordered his cabinet to gather information about the North Korean tests, check the security of vessels and aircraft as well as to prepare for any emergency.
Saturday's North Korean tests have become the third in a row after those conducted on 2 and 9 March - the first launches to occur in 2020.
North Korea's leader Kim Jong-un has said Pyongyang would not implement the ban on nuclear testing until the United States offered some concessions in the nuclear negotiations between Washington and Pyongyang that have stalled for some time already.