A medium-range ballistic missile fired by North Korea flew about 620 miles and landed in the Sea of Japan.
The US Strategic Command said North Korea fired two presumed Rodong missiles simultaneously on Wednesday.
It said initial indications reveal one of the missiles exploded immediately after launch, while the second was tracked over North Korea and into the Sea of Japan.
According to South Korea and Japan, one suspected Rodong missile lifted off from the North's western Hwanghae province and flew across the country before falling in waters between the Korean Peninsula and Japan.
Seoul's Joint Chiefs of Staff said that it "strongly condemns" the missile launch because it explicitly shows the North's intentions of being able to launch missile attacks on South Korea and neighbouring countries.
Japan's defence ministry said the missile landed inside Japan's exclusive economic zone, the 200-nautical-mile offshore area where a nation has sovereign rights for exploring and exploiting resources.
Japanese media reported it was the first North Korean missile that has splashed down in Japan's EEZ.
"It imposes a serious threat to Japan's security and it is unforgivable act of violence toward Japan's security," Prime Minister Shinzo Abe said.
North Korea has previously fired Rodong and other missiles into the sea but South Korean analysts say Wednesday's flight was one of the longest for a North Korean test.
Several North Korean rockets have gone further and even over Japan. But Pyongyang called them satellite launches while Washington, Seoul and Tokyo said they were disguised tests of missile technology.
After several failures, the North put its first satellite into space aboard a long-range rocket in December 2012 and conducted another successful satellite launch in February.
In June, North Korea, after a string of failures, sent another type of mid-range missile known as "Musudan" more than 870 miles high.
Analysts say the high-altitude flight meant North Korea had made progress in its push to be able to strike US forces throughout the region.
North Korea routinely conducts weapons tests, but the latest launch came after North Korea warned of unspecified "physical counter-actions" against a US plan to deploy an advanced missile defence system in South Korea by the end of next year.
Seoul and Washington officials said they need the Terminal High-Altitude Area Defence, or THAAD, system to better cope with what they call North Korea's increasing military threats.
North Korea called the system a provocation that it says is only aimed at bolstering US military hegemony in the region.
Pyongyang is expected to carry out more weapons launches in coming weeks to protest against annual US-South Korean military drills that begin later this month. North Korea describes the drills as an invasion rehearsal.
The Korean Peninsula remains in a technical state of war because the 1950-53 Korean War ended with an armistice, not a peace treaty.
About 28,500 US troops are stationed in South Korea and tens of thousands of more in Japan.