The North fired the missiles into the East Sea (Sea of Japan) from the country's east coast Sunday morning, a defence ministry official told AFP.
"Both landed in international waters beyond its sea border," the official said.
He did not elaborate on the type of the missile. But Yonhap news agency, citing a military official, said they were short-range Scud missiles with a range of about 500 kilometres (300 miles).
In Tokyo, Japanese Defence Minister Itsunori Onodera also told reporters that North Korea had launched a number of ballistic missiles.
He added that the Japanese government had lodged a protest with Pyongyang through its embassy in Beijing.
The launch came three days after Pyongyang fired what were believed to be three short-range missiles into the sea on Thursday.
The North did not officially confirm Thursday's launch, revealed by Seoul's military. But a day later, the state-run Korean Central News Agency hailed what it called the successful test of "cutting-edge" and high-precision missiles, watched by leader Kim Jong-Un.
- 'Warning message' from North -
The launches come only days ahead of Xi's state visit to Seoul to discuss issues including the North's disputed nuclear weapons programmes.
The July 3-4 trip -- Xi's first presidential journey to the Korean peninsula -- also marks the first time in almost two decades for a sitting Chinese leader to visit the South before having been to the North.
China is the isolated North's sole major ally and major economic lifeline that offers precious fuel and food to its wayward ally.
But ties have been tested by the North's pursuit of nuclear programmes in defiance of pressure from the international community including Beijing.
The North staged its third atomic test -- its most powerful so far -- in February 2013, triggering new sanctions and condemnation by UN Security Council members including China.
The latest missile launches were aimed at increasing pressure on Xi and South Korean President Park Geun-Hye ahead of their talks, said Shin In-Kyun, head of Korea Defense Network, a Seoul-based think tank.
"The two leaders will inevitably discuss how to curb the North's nuclear ambition and how to punish Pyongyang if it pushes ahead with the weapons programme," Shin said.
"And the North is sending a message of warning in advance, to prevent the leaders from criticising Pyongyang too harshly," he said.
Seoul and Washington have persistently called on Beijing to exert more pressure on the North to abandon its atomic weapons programme.
But despite China's growing frustration with the North, it fears the instability -- and flood of refugees -- that a collapse of the regime would bring.
The North has often launched short-range missiles or rockets to express anger at perceived provocations, including military drills held south of border.
In March, it conducted multiple launches of Scud missiles and rockets to coincide with annual joint army drills between Seoul and Washington.
The North also test-fired two medium-range ballistic missiles that flew 650 kilometres off its east coast, prompting a stern reaction from Washington and Seoul.
South Korea had condemned the missile launches as a "reckless provocation" but stopped short of calling for UN sanctions.