The test came just days after senior US officials praised North Korea and leader Kim Jong Un for showing restraint in not firing any missiles since late July.
The South Korean Office of the Joint Chiefs of Staff said the projectiles were launched from the North's eastern Kangwon province into the sea.
Later on Saturday, the South Korean Presidential Blue House said the North may have fired an upgraded 300-mm calibre multiple rocket launcher but the military was still analysing the precise details of the projectiles.
Pacific Command said the missiles did not pose a threat to the US mainland or to the Pacific territory of Guam, which North Korea had threatened earlier this month to surround in a "sea of fire".
Tensions had eased somewhat since a harsh exchange of words between Pyongyang and Washington after US President Donald Trump had warned North Korean leader Kim Jong Un he would face "fire and fury" if he threatened the United States.
North Korea's last missile test on July 28 was for an intercontinental ballistic missile designed to fly 10,000 km (6,200 miles). That would put parts of the US mainland within reach and prompted heated exchanges that raised fears of a new conflict on the peninsula.
Japan's Chief Cabinet Secretary Yoshihide Suga said the missiles did not reach its territory or exclusive economic zone and did not pose a threat to Japan's safety.
The South Korean and US militaries are in the midst of the annual Ulchi Freedom Guardian drills involving computer simulations of a war to test readiness and run until August 31.
The region where the missiles were launched, Kittaeryong, is a known military test site frequently used by the North for short-range missile drills, said Kim Dong-yub, a military expert at the Institute for Far Eastern Studies in Seoul.
"So rather than a newly developed missile, it looks to be short range missiles they fired as part of their summer exercise and also in response to the Ulchi Freedom Guardian drill," he said.
The United States and South Korea are technically still at war with the North because their 1950-53 conflict ended in a truce, not a peace treaty. The North routinely says it will never give up its weapons programmes, saying they are necessary to counter perceived US hostility. Washington has repeatedly urged China, North Korea's main ally and trading partner, to do more to rein in Pyongyang.
China's commerce ministry late on Friday banned North Korean individuals and enterprises from doing new business in China, in line with United Nations Security Council sanctions passed earlier this month.
The White House said Trump had been briefed about the latest missiles but did not immediately have further comment.
The US State Department did not immediately comment about the Saturday launches. Secretary of State Rex Tillerson earlier this week credited the North with showing restraint by not launching a missile since the July ICBM test.
Tillerson had said he hoped that the lack of missile launches or other “provocative acts” by Pyongyang could mean a path could be opening for dialogue "sometime in the near future."
Trump also expressed optimism earlier this week about a possible improvement in relations. "I respect the fact that he is starting to respect us," Trump said of Kim.
North Korea's state media reported on Saturday that Kim had guided a contest of amphibious landing and aerial strike by its army against targets modelled after South Korean islands near the sea border on the west coast.
The official KCNA news agency quoted Kim as telling its Army that it "should think of mercilessly wiping out the enemy with arms only and occupying Seoul at one go and the southern half of Korea."
A new poster on a North Korean propaganda website on Saturday showed a missile dealing "a retaliatory strike of justice" against the US mainland, threatening to "wipe out the United States, the source of evil, without a trace." On Wednesday, Kim ordered the production of more rocket engines and missile warheads during a visit to a facility associated with North Korea's ballistic missile programme.
Diagrams and what appeared to be missile parts shown in photographs published in the North's state media suggested Pyongyang was pressing ahead with building a longer-range ballistic missile that could potentially reach any part of the US mainland including Washington.