Seoul said a Russian A-50 warplane twice entered South Korean airspace near the disputed Dokdo islets -- which Japan calls Takeshima.
Seoul officials said they responded by scrambling F-15K and KF-16 fighters, which first issued warnings and fired flares. They fired 80 warning shots at the plane during the first breach, and 280 rounds during the second, a military official told AFP.
"We are assessing this incident in a very grave manner and will take a much tougher measure if it happens again," said National Security Advisor Chung Eui-yong, according to the Blue House spokeswoman.
Japan complained to both Moscow and Seoul over the incursion.
"We learned that Russian military planes flying over the Sea of Japan this morning twice violated our airspace near Takeshima," Chief Cabinet Secretary Yoshihide Suga told a regular press conference.
"Based on this knowledge, we made strong protests."
Suga, who said Japan also scrambled military jets, added South Korea's response was "extremely regrettable".
But South Korea's presidential Blue House insisted the disputed islets were an "integral part" of Korean territory "historically, geographically and under international law".
- Russia denies violation -
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Russia denied any airspace violation, insisting Seoul's complaint was based on an "arbitrarily established" air defence identification zone that Moscow did not recognise.
"It was not the first time that South Korean pilots tried to unsuccessfully interfere with the flights of the Russian aviation forces above the neutral waters of the Sea of Japan," the defence ministry said in a statement.
"Such 'zones' are recognized by neither international law nor Russia," it said, adding Moscow had repeatedly informed Seoul about it.
Russia later released a separate statement, saying Russian and Chinese long-range planes had staged a "first joint patrol mission in the Asia-Pacific region" to "deepen and develop Russian-Chinese relations".
"Both countries acted in strict accordance with international law," Moscow's defence ministry said in the statement, adding the event was "not aimed against third countries".
Seoul officials said the Russian plane first entered South Korean airspace just after 9:00 am (0000 GMT) and lasted three minutes.
It returned half an hour later, staying in South Korean airspace for four minutes, the military said.
At one point, the South Korean and Russian warplanes were just one kilometre apart, the official added.
The Russian plane "didn't appear to have hostile intention" during the manoeuvers, the military official said, as it flew "at constant speed and direction".
He added that more investigation is required to determine the motives for the breaches.
Dokdo, or Takeshima, are a series of rocky islets in the sea between South Korea and Japan that have long been disputed and the source of diplomatic friction between the two economic powerhouses.
They lie in rich fishing grounds that may also contain large deposits of natural gas.
Lingering tensions between Seoul and Tokyo over compensation for South Korean victims of Japan's wartime forced labour policy worsened this month when Tokyo restricted exports of high-tech materials to South Korea.