They were launched between 5:20 pm (0820 GMT) and 7:50 pm, with the first two fired from a base near the eastern port of Wonsan and the third from Sinsang-ri, the defence ministry said.
The hardline communist state has responded defiantly to UN condemnation of its long-range rocket launch on April 5 and its May 25 nuclear test, vowing to bolster its defences.
"They appear to be ground-to-ship missiles, which were launched into the East Sea (Sea of Japan)," a ministry spokesman told AFP, speaking of the first two launches.
"We have no detailed information now but there have been preparations for missile launches in the region."
Yonhap news agency said the third one was also a ground-to-ship missile.
The North issued a fresh warning to Japan on Wednesday to stay clear of some coastal areas during military exercises until 11 July.
According to Japan's Coast Guard, Pyongyang issued navigation bans for 10 areas in the Sea of Japan and the Yellow Sea, citing "military gunfire and bombardment training."
South Korea's JoongAng Ilbo newspaper, quoting an intelligence source, said the North in the coming days was likely to fire a series of short-range missiles.
Apart from ground-to-ship weapons with a range of 140 kilometres (88 miles), it said these would likely include Scud-B missiles with a range of 340 kilometres.
The North may also fire Rodongs, whose 1 300-km range would likely be shortened to some 400 km for the current round of testing, the paper predicted.
AFP
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