UN diplomats, speaking on condition of anonymity because the meeting was closed, said China and Rwanda also did not attend the closed session.
Russia's UN Mission said in a statement that the meeting on human rights and media freedom in Crimea was designed not to give an objective account of events in the region, "but to stage a biased propaganda show."
Russia sent troops into the Crimean Peninsula and annexed the strategic Black Sea region, which has a large Russian majority, on March 21.
She said the closed meeting gave diplomats their first opportunity to hear the concerns of "those who know what's going on in Crimea" about the impartiality of information and the human rights situation, especially for Crimean Tatars.
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Tatars, an ethnically Turkic and mainly Muslim group, was subjected to mass deportation from their native Crimea by Soviet leader Josef Stalin in 1944.
They started returning to the peninsular in the late 1980s with the breakup of the Soviet Union, and according to the most recent Ukrainian national census in 2001, the 245,000-strong Tatar community accounted for 12 percent of Crimea's population.
Lithuania's Kazragien said that Crimean Tatar human rights activist Mustafa Dzhemilev told Security Council members that the community is preparing for a referendum on greater autonomy.
He was joined at the closed meeting by Valentyna Samar, head of the Board of the Information Press Center in Crimea's capital Simferopol and chief editor of the Center of Journalistic Investigation.
The Russian Mission claimed that as part of Russia, the situation of human rights and media freedom in Crimea doesn't fall in the purview of the Security Council and undermined the "standing" and "image" of the UN's most powerful body.