"Ukraine's accession to NATO will cause a deep crisis in Russian-Ukrainian relations that will affect all-European security. Therefore, the West must also make a choice as to what kind of relationship with Russia is in its interests," Grigory Karasin said.
He said that Kiev's admission to NATO would require a review of Russia's own security policy.
"Our policy with regard to Ukraine will be based on respect, but we will develop it depending on Ukraine's further actions," he said.
He also said Russian and Ukrainian foreign ministers were to meet "in the very near future," and that a meeting of an intergovernmental commission on economic cooperation was to be held later in Kiev.
Russia's Foreign Ministry earlier said the ministers would meet on April 15 in Moscow.
Karasin was addressing a parliamentary hearing on the future of a Russian-Ukrainian friendship, cooperation and partnership treaty, which expires in exactly a year.
Some MPs have suggested that Russia should pull out of the treaty if Ukraine joins NATO's Membership Action Plan (MAP), a program that prepares countries for accession to the Western military alliance but does not guarantee membership.
U.S. President George W. Bush arrived in Ukraine late Monday and following a meeting with President Viktor Yushchenko told journalists on Tuesday: "We support MAP for Ukraine."
The visit is a stop-over before the April 2-4 NATO summit in Romania, which Russian President Vladimir Putin will also be attending, as a guest.
Ukraine's leaders requested in January to join NATO's Membership Action Plan.
However, despite Washington's unequivocal support for Ukraine's bid, membership is far from certain, with the majority of Ukrainians and a vocal minority in parliament resisting the plans, partly over fears of provoking its former Soviet master Russia.
The Kremlin threatened in February to target missiles at Ukraine if Kiev joins NATO and allows Western military facilities on its territory.
On Monday, thousands of people gathered on Kiev's Independence Square (Maidan Nezalezhnosti) to rally against Bush and NATO, displaying Communist flags and banners with the slogans: "NATO is worse than the Gestapo" and "Put Bush's bloody dictatorship under an international tribunal."
Yushchenko condemned the rallies, however, saying: "these were the flags that caused totalitarianism and suffering, the deaths of millions of people."
Ukraine's drive toward NATO membership has triggered domestic parliamentary opposition protests amid widespread antipathy toward the alliance. A survey published earlier this month said only 11% of Ukrainians supported the idea of NATO membership, while almost 36% were strongly opposed.
