"The suggestion that a president who has fled his country then has any authority whatsoever to invite the forces of a neighboring country into that country is baseless," he told U.K. lawmakers.
Ukraine's dire finances were a key issue in the protests that drove Yanukovych from power. On Tuesday, Russia's state-controlled natural gas giant Gazprom said it will cancel a price discount on gas it sells to Ukraine. Russia had offered the discount in December as part of Russian help for Ukraine. Gazprom also said Ukraine owes it $1.5 billion.
Ukraine's finance minister, who says the country needs $35 billion to get through this year and next, was meeting with International Monetary Fund officials.
Crimea still remained a potential flashpoint. Troops who had taken control of the Belbek air base in Crimea fired warning shots into the air Tuesday as around 300 Ukrainian soldiers who previously manned the airfield demanded their jobs back.
About a dozen troops warned the Ukrainians, who were marching unarmed, not to approach. They then fired several warning shots into the air and said they would shoot the Ukrainians if they continued toward them. The Ukrainians identified the gunmen as Russian and their vehicle had Russian military plates.
Part of the compound was still being held by Ukrainians.
"We are worried. But we will not give up our base," said Capt. Nikolai Syomko, an air force radio electrician holding an AK-47 and patrolling the back of the compound. He said the soldiers felt they were being held hostage, caught between Russia and Ukraine.
"They have shown restraint, despite the invasion of the Ukrainian homeland and a Russian government that has chosen intimidation," Kerry said of the Ukrainian soldiers.
The new Ukrainian government says troops that have overtaken Belbek and other Ukrainian military bases across Crimea were Russian. Putin denied it, saying the men were self-defense forces answering to Crimea's pro-Russian regional government.
Putin said Ukraine's 22,000-strong force in Crimea has dissolved and its arsenals have fallen under the control of the local government. Those officials claimed Tuesday that 5,500 Ukrainian soldiers had switched allegiances from Kiev to them. They were also seeking to move up a vote planned for March 30 on the region's status.
Ukraine's prime minister placed the blame for the current crisis with Russia squarely on the Kremlin, but expressed hope that a negotiated solution could be found. Prime Minister Arseniy Yatsenyuk told a news conference on Tuesday that both governments were talking again, albeit slowly.
"We hope that Russia will understand its responsibility in destabilizing the security situation in Europe, that Russia will realize that Ukraine is an independent state and that Russian troops will leave the territory of Ukraine," he said.
Russia is demanding the implementation of a Western-sponsored peace deal that Yanukovych signed with the opposition last month that set a new Ukrainian presidential election no later than December. Yanukovych fled the capital hours later and ended up in Russia, and the Ukrainian parliament then set the presidential vote for May 25.
The EU's 28 heads of state and government will hold an emergency meeting Thursday to decide whether to impose sanctions against Russia.
John Herbst, a former U.S. ambassador to Ukraine now at the Center for Complex Operations at the National Defense University, told the AP it was a critical time for Europe.
"It's a breach of international law, of national sovereignty, by a major power," Herbst said about Russia's actions in Crimea. "We haven't seen such a breach in Europe since the Nazis."
Sullivan reported from Crimea. Ivan Sekretarev in Sevastopol, Juergen Baetz in Brussels and Raul Gallego in Crimea contributed to this report.
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