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Putin spoke by phone with Mustafa Dzhemilev, a senior figure in the Crimean Tatar community, in what may have been an effort to ease their concerns over a referendum on Sunday in which Crimeans will be asked whether they want to join Russia.
Many Crimean Tatars, who make up about 12 percent of the population of the Black Sea peninsula, are strongly opposed to falling under Russia's control and want be governed from Kiev. Their leader has called for a boycott of the plebiscite.
"I, of course, expressed doubt about the expediency of holding this referendum, and about its legitimacy," Dzhemilev said in remarks to Ukraine's Channel 5 television.
The United States and European nations have said the Russian-backed vote would be illegitimate and are threatening to impose sanctions on Moscow if it goes ahead as planned. They say Russia has already seized control of Crimea.
"I told Putin that the issue of the territorial integrity of our country is very important," Dzhemilev said, according to the Ukrainian news agency Unian. Dzhemilev was in Moscow when he spoke to Putin, who was in the Black Sea resort of Sochi.
He said he told Putin Crimean secession would violate a 1994 pact in which Russia, Britain and the United States committed to assuring Ukraine's sovereignty and territorial integrity in return for its pledge to give up its ex-Soviet nuclear arsenal.
If this happens, "nobody will trust such agreements and there will be efforts to obtain nuclear weapons by every country with the financial wherewithal to do so - and Ukraine will be no exception," Unian quoted him as saying.
The 1994 treaty was part of an effort to ensure the Soviet collapse of 1991 did not lead to the proliferation of nuclear weapons. The superpower's breakup left Ukraine with the third-largest arsenal after the United States and Russia.
Exiled en masse by the Soviet authorities during World War Two, many Crimean Tatars are very wary of Russia.
Dzhemilev told Russian radio station Ekho Moskvy that Putin had promised that the security and rights of Crimean Tatars would be protected.
Putin said "measures will be taken to solve all the social and legal problems of Crimean Tatars that went unsolved by the Ukrainian authorities for many years," he was quoted as saying.
But Dzhemilev said he told Putin the best security guarantee would be the withdrawal of Russia forces from Crimea, Ekho Moskvy reported.
Russia denies sending troops into Crimea, saying armed men who have established what Western governments describe as "operational control" over the region are "self-defence units".