The missiles were fired from a region south of the capital Pyongyang just after noon (10.00 p.m. ET) and flew about 1,000 km (600 miles), hitting Japan's air defense identification zone, South Korea's Office of the Joint Chiefs of Staff said.
"We are still analyzing details but this is a grave threat to our nation's security, and we express deep concern," the Japan Defence Ministry said in a statement.
The launches drew immediate condemnation from the United States, which described them as "reckless," and diplomats said the U.N. Security Council will discuss them behind closed doors on Tuesday at Washington's and Tokyo's requests.
The missile launches were the latest in a series by the isolated North this year in violation of U.N. Security Council resolutions, supported by China, that ban all ballistic missile-related activities by the North.
Pyongyang rejects the ban as infringing its sovereign right to pursue a space program and self defense.
Shortly after the missile launches, South Korean President Park Geun-hye and Japanese Prime Minister Shinzo Abe met on the sidelines of the G20 summit and agreed to cooperate on monitoring the situation, a Japanese statement said.
The South's military said the missiles were medium-range Rodong-class, launched as a show of force timed to coincide with the G20 summit. The U.S. Strategic Command said in a statement that two of the three were presumed to be "intermediate range" ballistic missiles and that the third was still being assessed.
In 2014, the North fired two Rodong medium-range missiles just as Park and Abe were meeting U.S. President Barack Obama at the Hague to discuss responding to the North's arms program.
The latest missiles were launched from a region called Hwangju and came just hours after the leaders of South Korea and China met on the sidelines of the G20 summit in Hangzhou, China.
South Korea's Park told Chinese President Xi Jinping that the North's fourth nuclear test and its ballistic missile launches this year threatened regional peace and posed a challenge to South Korea's ties with China, Yonhap news agency reported earlier.
During the meeting, Xi reaffirmed China's commitment to realizing the denuclearisation of the Korean peninsula, China's state news agency Xinhua reported on Monday.
Xi also told Park that Beijing opposed the proposed deployment of a THAAD anti-missile system in South Korea, which Seoul and the United States have said is designed to counter an increasing missile threat from North Korea.
Park said that a THAAD deployment would not threaten any other country's security interests and would not be needed if the North's nuclear issue was resolved, Yonhap news agency said.
The United States "strongly" condemned the latest missile launches and called on North Korea to refrain from actions and rhetoric that raise tensions in the region, U.S. State Department spokesman John Kirby said in a statement.
"Today's reckless launches by North Korea threaten civil aviation and maritime commerce in the region," Kirby said, saying the United States would raise its concerns at the United Nations as well as at this week's East Asia Summit in Laos.
"Our commitment to the defense of our allies in the face of these threats remains ironclad," Kirby added in a reference to U.S. treaty allies South Korea and Japan.
In July, the North launched three missiles in a single day from the western region that flew across the country and into the sea off its east coast, flying about 500 km and 600 km (300-360 miles).