The launches came hours after Washington deployed B-1B bombers for combined air drills with Seoul and a day before the allies wrap up their annual Ulchi Freedom Shield exercises, which always infuriate Pyongyang.
The North's army said the missiles were fired late Wednesday in a "tactical nuclear strike drill simulating scorched earth strikes at major command centers and operational airfields" across the border in South Korea.
The "tactical ballistic missiles" were fired northeastward from Pyongyang International Airport and "correctly carried out (their) nuclear strike mission", the army said in a statement carried by the official Korean Central News Agency.
"The drill is aimed to send a clear message to the enemies," it added.
South Korea's Joint Chiefs of Staff said it detected two short-range ballistic missiles fired from the North towards the East Sea, also known as the Sea of Japan, just before midnight.
The missiles flew around 360 kilometres before landing in the water, and the launches are now being analysed by South Korean and US intelligence officials, the JCS said in a statement.
Tokyo said both missiles were believed to have fallen near the east coast of the Korean peninsula and outside Japan's exclusive economic zone.
Pyongyang's army also staged command-level drills on Tuesday in response to the US-South Korean exercises, during which leader Kim Jong Un visited a training command post, KCNA said in a separate report.
The drill simulated repelling a sudden invasion and launching a counterattack to occupy "the whole territory of the southern half", it added.
Kim detailed future war plans, including "making simultaneous super-intense strikes" at core military posts to cause "socio-political and economic chaos".
Photos carried by the official Rodong Sinmun newspaper showed Kim, surrounded by military officers, pointing to what appeared to be South Korea on a blurred map of the Korean peninsula.
- 'Irreversible' nuclear power -
Leif-Eric Easley, a professor at Ewha University in Seoul, said North Korean missile launches during US-South Korean exercises were not unusual, but noted they were being carried out at "odd hours".
Pyongyang may want to demonstrate its ability to attack at any time and from many directions, or simply to complicate the allies' missile tracking and analysis, said Easley.
"Or Kim Jong Un could be suffering from insomnia and testing the readiness of subordinates at all hours of the night," he added.
North Korea has conducted a record number of weapons tests this year, and last week carried out its second failed attempt to put a spy satellite into orbit.
Seoul and Washington have ramped up defence cooperation in response, staging joint military exercises with advanced stealth jets and US strategic assets.
On Tuesday, the United States, South Korea and Japan held a trilateral naval missile defence exercise, their fourth such training this year, according to the Yonhap news agency.
Relations between the two Koreas are at their lowest point in years, and diplomacy is stalled after failed attempts to discuss Pyongyang's denuclearisation.
Kim has declared North Korea an "irreversible" nuclear power and called for ramped-up arms production, including of tactical nuclear weapons.
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