Russian Prime Minister Dmitry Medvedev said Ukraine’s interim authorities had conducted an “armed mutiny”.
And the Russian foreign ministry said dissenters in mainly Russian-speaking regions faced suppression.
Earlier, Ukraine’s interim interior minister said an arrest warrant had been issued for ousted President Viktor Yanukovych.
Ukraine’s parliament voted to remove Viktor Yanukovych on Saturday. His whereabouts are unknown but he was reported to have been in the Crimean peninsula on Sunday.
Russia has already recalled its ambassador to Ukraine for consultation.
Unrest in Ukraine began in November when Viktor Yanukovych rejected a landmark association and trade deal with the EU in favor of closer ties with Russia.
Dmitry Medvedev, quoted by Russian news agencies, suggested that Western countries that accepted Ukraine’s new authorities were mistaken.
“The legitimacy of a whole number of organs of power that function there raises great doubts,” he said.
“Some of our foreign, Western partners think otherwise. This is some kind of aberration of perception when people call legitimate what is essentially the result of an armed mutiny.”
He added: “We do not understand what is going on there. There is a real threat to our interests and to the lives of our citizens.”
Ukraine’s foreign ministry quickly responded to Dmitry Medvedev’s comments on Russian citizens in Ukraine, saying his concerns were “unfounded”.
However, Russia’s foreign ministry also issued a strongly worded statement saying a “forced change of power” was taking place in Ukraine and accused interim leaders of passing new laws “aimed at infringing the humanitarian rights of Russians and other ethnic minorities”.
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