The missiles were fired just before midnight into the Sea of Japan, according to the South Korean military.
The type of missiles launched is still being analyzed, Yonhap said.
“As we tighten control and vigilance against further provocations, our military maintains a stand-by posture in close cooperation with the United States,” South Korea’s Joint Chiefs of Staff said in a text message to reporters.
US national security spokesman John Kirby declined to comment to reporters in Washington when the news broke.
North Korea’s ballistic missiles are prohibited by United Nations Security Council resolutions that have imposed strict sanctions on the nuclear-armed country.
The military exercises between South Korea and the United States involve at least one US B-1B strategic bomber, which flew over the Korean peninsula early on Wednesday, according to Yonhap.
The United States, South Korea and Japan also conducted a naval missile defense exercise on Tuesday, angering Pyongyang.
Washington, Seoul and Tokyo have stepped up their defense cooperation in recent months in response to increased missile provocations by North Korea.
B-1B bombers conducted separate aerial exercises with South Korean and Japanese warplanes early Wednesday.
So far this year, Pyongyang has set a record for weapons tests.
With information from AFP and Reuters