Putin told Obama there was a "real threat weighing on the lives and the health of Russian citizens" in Ukraine, according to a Kremlin statement.
The Russian president accused the new government in Kiev of supporting "criminal actions by ultranationalists", the Kremlin said.
The two leaders spoke yesterday by telephone after Russia's parliament authorised military action in Ukraine in a dramatic escalation of tensions.
The Kremlin statement said the conversation was instigated by the US side and focused on the "extraordinary situation in Kiev".