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NATO has expelled two Russian diplomats from its headquarters in Brussels over accusations of espionage, officials said Thursday, threatening a new rift between the two sides just as relations were beginning to improve.

NATO would not publicly comment on the move, but the timing was striking. On Wednesday, NATO and Russia resumed their first formal contacts since they had been ruptured over the war last August between Russia and neighboring Georgia.

Dmitri O. Rogozin, Russia’s ambassador to NATO, called the expulsions a “clear-cut provocation,” saying that Russia was not engaging in spying and indicating that it would retaliate.

The identities of the diplomats expelled suggested that NATO considered the matter serious. One is a senior official in Russia’s mission to NATO, and the other is the son of Russia’s ambassador to the European Union, which is also based in Brussels, Belgium.

It seems likely that Russia will seek to expel two Western diplomats from Moscow, as is customary in these kinds of diplomatic rows. The question is whether it will escalate tensions by once again breaking off official ties with NATO. The Russian foreign minister, Sergey V. Lavrov, is scheduled to conduct high-profile talks with his NATO counterparts in May.

The two sides had already been grappling over NATO military exercises scheduled in Georgia in May and June. Russia’s president, Dmitri A. Medvedev, sharply criticized the exercises, which had been long planned and are relatively modest in size. When NATO would not cancel them, Russia withdrew from a meeting of military officials.

Georgia would like to join NATO over the objections of Russia, which has contended that the alliance is moving into areas that have traditionally been within Moscow’s zone of influence. The August war, which Russia easily won, broke out over two separatist regions of Georgia that have close ties to Russia.

Also Thursday, Russia signed an agreement with the two regions, South Ossetia and Abkhazia, giving Russia authority to guard their borders. Both Georgia and its Western allies said the agreement violated the cease-fire that ended the war.

In Brussels, Rogozin said that after a meeting Wednesday of the NATO-Russia Council, he was asked to speak privately with the secretary-general of NATO, Jaap de Hoop Scheffer.

“In the course of this,” Rogozin said, “it was stated to me the following: NATO is outraged at Russia over its carrying out of spying activities against NATO, and also the member countries of the alliance.”

Rogozin said the two Russian diplomats whose NATO credentials were revoked — Viktor N. Kochukov, a senior political officer, and Vasily V. Chizhov — had nothing to do with spying. Chizhov is the son of Vladimir A. Chizhov, Russia’s ambassador to the European Union, officials said.

Rogozin contended that the NATO decision was in response to an espionage scandal in Estonia, a NATO member and former Soviet republic. A senior Estonian security official was convicted there on charges of spying for Russia.