South Korea fired warning shots at a Russian A-50 military aircraft that entered its airspace on Tuesday, its Ministry of Defence said.
Officials said the plane violated the airspace over the Dokdo/Takeshima islands, which are occupied by Seoul but also claimed by Japan.
South Korea’s Ministry of Defence said it scrambled fighter jets in response and fired 360 warning shots.
Russia has denied violating the country’s airspace.
It says it was carrying out a planned drill over international waters.
This is the first incident of its kind between Russia and South Korea.
South Korea’s military said the aircraft was one of three Russian and two Chinese military warplanes that entered the Korea Air Defense Identification Zone (KADIZ), where overseas aircraft must identify themselves beforehand, on Tuesday morning.
Russian and Chinese bombers and reconnaissance planes have occasionally entered the zone in recent years.
However, South Korea said one of the Russian planes flew further and entered the country’s territorial airspace at around 09:00 local time (00:00 GMT).
South Korean F-15k and F-16k planes were deployed to intercept it.
The head of South Korea’s National Security Office, Chung Eui-yong, has lodged a strong objection with the Security Council of Russia, and asked the council to take appropriate action.
“We take a very grave view of this situation and, if it is repeated, we will take even stronger action,” the South Korean president’s office quoted Mr Chung as saying.
There has been no comment from China.