The sixth in 12 days, the missile launch was the first since North Korea fired an intermediate-range missile over Japan on Tuesday.
South Korea's Joint Chiefs of Staff and the Japanese government both reported the launch.
"This is the sixth time in the short period just counting the ones from the end of September," Japanese Prime Minister Fumio Kishida said.
"This absolutely cannot be tolerated."
The launch came about an hour after North Korea condemned the US for talking to the UN Security Council about the "just counter-action measures of the Korean People's Army on South Korea-US joint drills".
The North Korean Foreign Ministry also condemned Washington for repositioning a US aircraft carrier in the waters off the Korean Peninsula, saying it posed a serious threat to stability.
US and South Korea in show of force after North Korea's missile launch - in pictures
The USS Ronald Reagan and its strike group of warships was abruptly sent after South Korea and the US military conducted rare missile drills east of North Korea.
The US accused China and Russia on Wednesday of enabling North Korean leader Kim Jong-un by blocking attempts to strengthen UN Security Council sanctions on Pyongyang over its nuclear weapons and ballistic missile programmes.
South Korea missile blows up a day after North's launch over Japan - video
Tokyo lodged a "vehement protest" with North Korea through delegations in Beijing, Japanese Defence Minister Yasukazu Hamada said.
The first missile on Thursday probably flew to an altitude of about 100 kilometres and a range of 350km.
The second had an estimated altitude of 50km and covered 800km, probably flying in an irregular trajectory, Mr Hamada said.
North Korea fires ballistic missile over Japan - video
Many of North Korea's most recent short-range ballistic missiles are designed to fly on a lower, depressed trajectory and manoeuvre, complicating efforts to detect and intercept them.
"North Korea has relentlessly and unilaterally escalated its provocation, especially since the beginning of this year," Mr Hamada said.
South Korea's joint chiefs said the missiles were launched from near the North Korean capital of Pyongyang.