Seoul's Ministry of National Defence said that the South Korean fighter jets fired a warning shot at a Russian military aircraft that it said had entered the country's airspace.
According to South Korean military, a Russian military aircraft violated South Korea's airspace above the East Sea twice on Tuesday.
There were no immediate clarifications on the type of aircraft, however, the South Korean Joint Chiefs of Staff said that it was a bomber according to the Yonhap news agency.
The head of the South Korean National Security Office, Chung Eui-yong, expressed on Tuesday protest to Russian Security Council Secretary Nikolai Patrushev over Russian warplane's alleged violation of South Korea's airspace.
"We see this situation as an extremely serious one. If such behavior is repeated, we will introduce much tougher measures," Chung said, as quoted by the South Korean presidential administration.
Chung expressed "resolute protest" in his conversation with Patrushev, according to the administration.
"We call on the [Russian] Security Council to assess the situation and take appropriate steps," Chung added.
There were no immediate comments on the matter from Russian military.
The Russian Defence Ministry has repeatedly said that all flights of Russian military aircraft are carried out in full accordance with international law, and the rules for the use of airspace over neutral waters.