The firing of the missiles, reported to be Scuds with a range of 500 kilometres (312 miles), follow a series of missile launches earlier this week by the isolated Stalinist state.
"North Korea launched two missiles this morning," the Joint Chiefs of Staff said in a statement.
The missiles were launched between 8:00 am and 8:30 am (2300-2330 GMT Friday) from Kitdaeryong Base near the eastern port of Wonsan into the East Sea (Sea of Japan), it said.
"The military, on the basis of a strong joint defence alliance with the United States, is fully prepared to fend off any threats or provocations by the North," it said.
An unidentified government official quoted by Yonhap news agency said both missiles were believed to be Scuds with a range of 500 kilometres (312 miles), which would allow the North to strike almost anywhere in South Korea.
North Korea fired four short-range missiles on Thursday into the Sea of Japan but the range of those missiles was estimated to be only around 120 km.
"The Scuds fired today impose a greater security threat to us because of their longer ranges," the official was quoted as saying by Yonhap.
"Thursday's missile tests were apparently made as part of a military drill but today's launches, which came on the eve of the US Independence Day, are believed to be aimed at political purposes," the official said.
Japan condemned the latest missile launches as a "serious act of provocation".
"It is a serious act of provocation against the security of neighbouring countries, including our country," Chief Cabinet Secretary Takeo Kawamura was quoted by Jiji Press as saying.
The government's top spokesman also said the act was against a UN Security Council resolution, according to Jiji.
Analysts said the North was flexing its military muscle amid tough international sanctions imposed on Pyongyang over its nuclear weapons and missile programmes.
Baek Seung-Joo of the Korea Institute for Defence Analyses said the North test fires missiles three to four times each year to improve technology and maintain missile exports.
"Today's launches were part of a usual military drill but by firing 500km-range Scuds, the North was clearly displaying its ability to strike back against any international sanctions involving military means," Baek told AFP.
He said, however, there is no sign of the North preparing to fire another long-range missile.
The North has made a series of bellicose moves this year. A long-range rocket launch on April 5 was followed by the nuclear test -- the second since 2006 -- on May 25.
In the days after its atomic test, Pyongyang fired a total of six short-range missiles, renounced the truce in force on the Korean peninsula for half a century and threatened possible attacks on Seoul.
When the United Nations tightened sanctions on its missile and atomic activities, the North vowed to build more nuclear bombs.
US and South Korean officials believe ailing leader Kim Jong-Il, 67, is staging a show of strength to bolster his authority as he tries to put in place a succession plan involving his youngest son Jong-Un.
This week's missile launches were the first military action the hardline communist state had taken since the United Nations on June 12 imposed tougher sanctions for the second nuclear test.