The first missile was launched at 5.06 a.m., and the second at 5.27 a.m., from the Kalma area in the North's eastern port of Wonsan, according to the Joint Chiefs of Staff (JCS).
Both are estimated to have flown about 250 km at an approximate altitude of 30 km, the JCS said, adding that the South Korean and US militaries were analyzing more details, Yonhap news agency reported.
The launch come six days after North Korea fired two short-range ballistic missiles from the same area into the East Sea in its first provocation since May.
Those missiles flew some 600 km at an altitude of around 50 km and were identified as "KN-23", or the North's version of Russia's Iskander ballistic missile.
"Successive missile launches by North Korea are not conducive to efforts to reduce tensions on the Korean Peninsula, and we call for a halt to these acts," the JCS said in a statement.
A JCS official told reporters that Wednesday's missiles were fired from a transporter erector launcher (TEL), as was the case with the launch last week, adding that the latest incident appears to be a test of the weapons, given their relatively low altitude.
He added that the missiles appeared to be similar to those launched last week, though the military was analyzing data related to the pattern of their flight.
After last week's missile firings, North Korea's state media had said that those launches, held under the supervision of leader Kim Jong-un, were designed to send a "solemn" warning to South Korea over its plan to conduct joint military drills with the US in August and purchase high-tech fighter jets from the ally.
South Korea held a National Security Council (NSC) meeting and expressed "strong" concerns over the firings, urging Pyongyang to "stop acts that could heighten tensions and hamper efforts to bring peace to the Korean peninsula".
Foreign Minister Kang Kyung-wha also said that North Korea's latest missile firings were not helpful in easing military tensions or in keeping the momentum for denuclearization talks.
The US responded cautiously.
"We are aware of reports of a missile launch from North Korea and we will continue to monitor the situation," a State Department spokesperson told Yonhap news agency on condition of anonymity.
The series of launches comes as Washington has sought to restart working-level talks on dismantling the North's nuclear and ballistic missile programmes in line with an agreement reached when US President Donald Trump and Kim Jong-un held a surprise meeting at the inter-Korean border in June.
Despite last week's missile launches, the US has remained upbeat about the prospects for talks with the North, with Trump dismissing last week's missiles as "smaller ones" that many countries test.
( With inputs from IANS )