South Korea's military said the missile reached an estimated altitude of about 770km (478 miles) and travelled 3,700km before landing in the sea off Hokkaido.
Japan's PM Shinzo Abe said his country would "never tolerate" such "dangerous provocative action".
"If North Korea continues to walk down this path, it has no bright future," he said in a statement.
PM Shinzo Abe said North Korea had "trampled on the international community's strong, united resolve toward peace"
US Secretary of State Rex Tillerson also condemned the launch, which contravened UN sanctions.
He put the burden of response on China and Russia, nuclear-armed North Korea's main economic partners, saying they "must indicate their intolerance for these reckless missile launches by taking direct actions of their own".
Minutes after the launch, South Korea fired two ballistic missiles into the sea in a simulated strike on North Korea, reported Yonhap news agency.
President Moon Jae-in held an emergency meeting of his national security council, where he said that dialogue with the North was "impossible in a situation like this", reported Yonhap news agency.
Mr Moon was elected earlier this year after campaigning partly on conducting more dialogue with Pyongyang.
The projected path of the ballistic missile over Hokkaido is shown on TV in Japan
The South Korean military said the latest launch - the first since sanctions were tightened this week - took place from the Sunan airfield north of Pyongyang just before 07:00 local time (22:00 GMT on Thursday).
As with the last launch, it flew over Japan's northern Hokkaido island before splashing down in the Pacific Ocean.
Sirens sounded across the region and text message alerts were sent out warning people to take cover.
According to the initial estimates, the missile flew considerably higher and further than the one fired on 29 August, which Pyongyang had warned was only "the first step" in its military operations in the Pacific.
Observers said it was likely an intermediate range ballistic missile (IRBM), though Japanese officials said there was still a possibility it had been an intercontinental ballistic missile (ICBM).
Japan's chief cabinet secretary Yoshihide Suga said there had been no reports of damage to aircraft or ships.
The UN Security Council will meet on Friday in New York at the request of Japan and the US.
North Korea, which insists it needs a nuclear and weapons programme to ensure its survival, has repeatedly conducted missiles launches in recent months, disregarding UN sanctions.
North Korea said in early September that it had tested a "missile-ready" hydrogen bomb
It also conducted its sixth nuclear test two weeks ago, which it claimed was a hydrogen bomb, the most powerful weapon ever made.
Fresh UN sanctions were imposed in response targeting the few remaining international trade links North Korea has.
But these appear to have done nothing to stop North Korea's weapons development, nor its fiery warnings.
On Thursday, it threatened to "sink Japan and turn America to ashes".
North Korea's missile programme
- Pyongyang has been developing weapons, initially based on the Soviet-developed Scud, for decades
- Conducted short and medium-range missile tests on many occasions, sometimes to mark domestic events or periods of regional tension
- Pace of tests has increased in recent months; experts say North Korea appears to be making significant advances towards building a reliable long-range nuclear-capable weapon
- On 3 September, North Korea said it tested a hydrogen bomb that could be miniaturised and loaded on a long-range missile