It is the first launch of a Nodong missile since 2009 and marks a step up from the short-range rockets Pyongyang has fired in recent weeks.
The launches also came on the fourth anniversary of the sinking of a South Korean warship.
Washington and Seoul have condemned the launch, which violates UN resolutions.
The US State Department described the launch as "a troubling and provocative escalation".
"We urge North Korea to exercise restraint and refrain from further threatening actions," deputy spokeswoman Marie Harf said in a statement.'Grave provocation'
The South Korean defence ministry said the missiles were fired from the Suckon region north of Pyongyang and flew for about 650km (400 miles) before falling into the sea off the east coast of the Korean Peninsula.
"This missile is capable of hitting not only most of Japan but also Russia and China," ministry spokesman Kim Min-seok said.
The ministry described it as a "grave provocation".
In recent weeks, North Korea has launched multiple short-range missiles - actions which have coincided with annual US-South Korea military exercises.
But this is the first launch of a Nodong missile - which has a range of about 1,000km - since 2009. A similar launch also took place in 2006.
Ballistic missile launches by Pyongyang are banned by the United Nations.
North Korea has conducted three nuclear tests, the most recent in February 2013. It is also developing a three-stage missile that experts believe could be capable of hitting parts of the US.
But it is not yet believed to have the expertise to miniaturise a nuclear weapon so it could be delivered via a missile.
The US State Department said North Korea did not issue any maritime notification warning of its latest test.
"We are closely co-ordinating with our allies and partners, including in the UN Security Council, to take the appropriate measures in response to this latest provocation and to address the threat to global security posed by the DPRK's [North Korea's] nuclear and ballistic missile programmes," the statement said.
The launches took place in the early hours of Wednesday, which marks four years since South Korea's Cheonan warship sank with the loss of 46 lives near the disputed inter-Korean western maritime border.
South Korea says North Korea torpedoed the ship. North Korea denies any role in the incident.
They also came just hours after US President Barack Obama met his South Korean counterpart, Park Geun-hye, and Japanese Prime Minister Shinzo Abe at the nuclear summit in The Hague for talks that focused on North Korea's nuclear ambitions.
It was the first meeting between Ms Park and Mr Abe since both took office, amid strained ties over historical and territorial issues.
Mr Obama pledged his "unwavering commitment" to Tokyo and Seoul in the face of North Korea's nuclear programme.
Pyongyang says its rocket tests are self-defence exercises and says the military drills by Washington and Seoul are invasion preparations.
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