South Korea’s government said Wednesday that Moscow had expressed “deep regret’’ over the incident that prompted South Korean jets to fire warning shots near a Russian military plane, but a Russian spokesman countered that his country had not formally apologized.

The contrasting — if not quite contradictory — statements, and Russian objections to parts of the South Korean account, illustrated the tension over the most serious confrontation in years between the two nations.

On Tuesday, a Russian military jet flew twice into South Korea’s territorial airspace, officials in Seoul said, and when it did not respond to radio warnings, South Korean planes fired shots to ward it off. Russia denied any violation of another country’s airspace.

But Wednesday, Yoon Do-han, a spokesman for the South Korean president, told reporters that a Russian military attaché in Seoul had conveyed Moscow’s “deep regret’’ about the incident and had said that the Russian plane mistakenly deviated from its flight plan. He did not describe the Russian statement as an outright apology.

A short time later, the spokesman for the Russian Embassy in Seoul took issue with that account, although his objections were not entirely clear.

The news agency Interfax quoted the spokesman, Dmitry Bannikov, as saying that Russian officials had seen reports on Yoon’s comments, and that “there are many things in them that aren’t true.’’

“The Russian side did not issue an official apology,’’ Bannikov noted, according to the agency.

That appeared to leave open the possibility that the Russians were apologetic in private.

South Korean officials said that the Russian plane involved in the incident was a Beriev A-50 equipped with powerful long-range radar to track and coordinate the movements of multiple aircraft.

It was in a group of Russian and Chinese military planes conducting a joint operation over the Sea of Japan, an indication of growing cooperation between those two powers.

The confrontation took place near a cluster of islands controlled by South Korea but also claimed by Japan.

Moscow said Wednesday that it had been involved in a separate confrontation on the Korean Peninsula after North Korea seized a Russian fishing ship and its crew.

A statement posted on Facebook by the Russian Embassy in Pyongyang said that North Korea had made the seizure July 17, claiming that the vessel had violated rules for entering the country. The crew members were said to include 15 Russians and two South Koreans.

The Russians said that they had visited the Russian crew members and were working with North Korea to resolve the matter.