The military said it fired 10 flares and 80 machine-gun rounds during the alleged first violation.
It said the Russian plane then left before circling back round again, when it was met by 10 more South Korean flares and 280 machine-gun rounds.
In its statement, Russia only mentioned two bomber planes. It did not specifically acknowledge the accusation that it had also sent an A-50 that had strayed.
Known as Dokdo (Solitary islands) in Korea, Takeshima (Bamboo islands) in Japan
Claimed by Japan and South Korea, but occupied by South Korea since 1954
Just 230,000 sq m in size
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Media captionA BBC report from the islands in 2012
What has the response been?
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.
The Japanese government has lodged a complaint against South Korea and Russia.
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.”
China has insisted South Korea’s air defence identification zone is not territorial airspace and so all countries can move within it, according to Reuters news agency.
So was this a mistake? Did this Russian plane accidentally stray into South Korean territory?
Officials in South Korea said it was an A-50 aircraft, a type of warning and control plane that is capable of carrying out surveillance and tracking targets on the ground and in the air.
It encroached on South Korean territorial airspace not just once – but twice.
It is also worth noting that the Russian aircraft appeared to have been taking part in exercises with the Chinese. In recent years, Seoul has become increasingly concerned about China’s incursion in its airspace, including the use of spy planes, and has raised the issue with Beijing.
Last year, China’s People’s Liberation Army took part in Russia’s large-scale VOSTOK military exercises for the first time. It was a chance to show off their alliance and combined strength. They have done that again now, over the Korean peninsula – perhaps either testing or prodding a US ally, just as Donald Trump’s National Security Advisor John Bolton arrives in Seoul.
Flying over Dokdo is controversial. The island is occupied by South Korea but also claimed by Japan, which calls it Takeshima. The two sides are also currently locked in an escalating and bitter trade dispute.
This incident may demonstrate just how isolated South Korea could be in the region – but also that Seoul will take action to defend its territory when provoked.