"North Korea fired one short-range missile at around 5.34 a.m. and the other at 5.57 a.m., from Hodo Peninsula near its eastern coastal town of Wonsan into the East Sea," the Joint Chiefs of Staff (JCS) was quoted as saying by Yonhap news agency.
Pyongyang's move comes after anger over planned military exercises between South Korea and the US, an annual event. The North warned they could affect the resumption of denuclearization talks.
One missile flew around 430 km and the other travelled around 690 km, a JCS officer said, adding that both flew at an altitude of around 50 km.
"We've found some features that indicate that the second one could be a new type, which requires more analysis and assessment," the officer said.
They were presumed to have been fired from a Transporter Erector Launcher (TEL) and landed in the East Sea, the officer said.
"We believe that (North Korean leader) Kim Jong-un has recently stayed in the region, and summertime military drills are now under way in the North."
In response to Thursday's launches, South Korea's Defence Ministry called on Pyongyang "to stop such acts that do not help efforts to ease military tensions on the Korean Peninsula" and vowed to ramp up surveillance in close cooperation with the US.
The Foreign Ministry also said it was in close consultations with the US and Japan in sharing up-to-date information and analysis on the missile firings.
South Korea will continue its diplomatic efforts for the resumption of denuclearization talks for a swift outcome and plans to discuss the matter with China and Russia, the Ministry added.
Japan's Defence Minister Takeshi Iwaya said the launches did not reach Japanese waters and had no immediate impact on its national security.
In June, the North Korean leader and US President Donald Trump agreed to resume their working-level talks within a few weeks, when they met at the inter-Korean border.
Negotiations on North Korea's nuclear weapons programme have been stalled since February after the summit between Trump and Kim ended without results.
Pyongyang has reportedly not responded to Washington's offer for dialogue. Instead, it has also called the US and South Korea to cancel their combined military exercise in August, warning that the drill would affect ongoing efforts to resume its nuclear talks.
Despite such warnings, Seoul and Washington have said they are scheduled to launch the exercise as planned.
( With inputs from IANS )