The firing of the missiles, reported to have a range of up to 500 kilometres (312 miles), follow a series of missile launches earlier this week by North Korea.
A spokesperson of the South Korean Defence Ministry claimed that the first two of the three missiles were launched between 8 and 8.30 am, while the third one was fired at 10:45 am local time.
She said all three missiles were launched from the Kitdaeryong Base, near the eastern port of Wonsan, into the East Sea (Sea of Japan).
South Korea's Yonhap news agency said the first two missiles were Scuds.
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.
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 Japanese government's top spokesman said the act was also against a UN Security Council resolution, according to Jiji.
North Korea has made a series of bellicose moves this year. It launched a long-range rocket on Apr 5 and followed it up with a nuclear test on May 25.
Thereafter, the country has fired a total of six short-range missiles, renounced the truce on the Korean peninsula that has been in place for for half a century and threatened to attack South Korea.