Ban Ki-moon will express "grave" concerns directly to Russian leader Vladimir Putin by telephone, his spokesman said, as tensions escalated in Ukraine.
"He calls for an immediate restoration of calm and direct dialogue between all concerned to solve the current crisis," UN spokesman Martin Nesirky told reporters in New York.
"The secretary general wants to speak to President Putin directly to express his concerns. But also to hear directly from President Putin his assessment of the situation."
"We are deeply concerned about the situation, especially the developments over the last 24 hours," British ambassador Mark Lyall Grant told reporters on his way into the session.
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"That is why we have called this emergency session to find out what justification Russia claims to have for the actions they are taking at the moment," he added.
The UN secretary general reiterated his call "for the full respect for, and preservation of, the independence, sovereignty and territorial integrity of Ukraine".
"The most important thing is to raise concerns about what is happening on the ground," said Raimonda Murmokaite, ambassador of Lithuania, the current president of the Council.
The UN envoy to Ukraine, Robert Serry, said today he was leaving the country and ruled out a visit to the Crimea region as requested by Ban following emergency talks yesterday.
"I have since been in touch with the authorities of the autonomous republic of Crimea and have come to the conclusion that a visit to Crimea today is not possible," Serry said.
Ukrainian Defense Minister Igor Tenyukh today accused Russia of sending 30 armored personnel carriers and 6,000 additional troops into Crimea.
Dozens of pro-Russian armed men in full combat gear patrolled outside the seat of power in Crimea's capital Simferopol.
Similar gunmen seized the city's parliament and government buildings on Thursday and took control of its airport and a nearby military base yesterday.