It was the first time a Russian military aircraft had violated South Korean airspace, an official at the South Korean Ministry of National Defence said in Seoul.
The incident, which also involved China and Japan, could complicate relations and raise tensions in a region that has for years been over-shadowed by hostility between the United States and North Korea.
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A separate Russian A-50 airborne early warning and control aircraft later twice violated South Korean airspace over Dokdo just after 9 am according to the South Korean military.
Russia's defence ministry said two Tu-95 strategic bombers carried out a planned flight, but denied that they had violated South Korean airspace and said it did not recognise South Korea's KADIZ.
There were no warning shots from the South Korean fighters, the Russian defence ministry said in a statement, which made no mention of any A-50 aircraft.
The Russian ministry said two South Korean F-16 fighter planes carried out "unprofessional manoeuvres," crossing the path of Russian bombers and did not communicate with them.
"It was not for the first time that South Korean pilots tried unsuccessfully to prevent Russian aircraft from flying over the neutral waters of the Sea of Japan," the ministry said.
A South Korean defence ministry spokesman did not directly address the Russian accusation of reckless behaviour, but said that South Korea never said the Tu-95 bombers had violated its airspace.
China's foreign ministry said South Korea's air defence identification zone was not territorial airspace and all countries enjoyed freedom of movement in it.
South Korea's top security adviser, Chung Eui-yong, lodged a strong objection with Nikolai Patrushev, secretary of the Security Council of Russia, asking the council to assess the incident and take appropriate action, South Korea's presidential office said.
"We take a very grave view of this situation and, if it is repeated, we will take even stronger action," Chung said, according to South Korea's presidential office.
'Tactical Action'
South Korea's foreign ministry summoned Russian Deputy Chief of Mission Maxim Volkov and Chinese Ambassador Qiu Guohong to lodge a stern protest and strongly urge them to prevent a recurrence, said ministry spokesman Kim In-chul.
Separately, Japan lodged a complaint with both South Korea and Russia over the incident, Chief Cabinet Secretary Yoshihide Suga said.
"In light of Japan's stance regarding sovereignty over Takeshima, the South Korean military aircraft's having carried out warning shots is totally unacceptable and extremely regrettable," Suga told reporters in Tokyo.
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