"The words about intimidation from Russia are, at the very least, inappropriate," Mikhail Kamynin, a spokesman for the ministry, said.
Responding to Russian President Vladimir Putin's recent statement that Russia could retarget its missiles against Ukraine if the former Soviet republic joined NATO, Rice said on Wednesday that the "reprehensible rhetoric that is coming out of Moscow is unacceptable, and it's not helpful to a relationship that actually has some positive aspects."
Rice also said that the U.S. was "devoted to the independence and sovereignty of Ukraine and of other states that were once a part of the Soviet Union."
"The Soviet Union had all these parts [former Soviet republics], but that was another point in time and it is gone forever, and I hope that Russia understands that," she went on.
Commenting on Ukraine's bid for NATO membership, Putin said during a meeting with Ukrainian counterpart Viktor Yushchenko in Moscow earlier this week that it was the country's internal affair, but called on Kiev to think about the consequences of the move.
"It is terrifying even to think that in response [to Ukraine allowing anti-missile defenses to be deployed on its territory] Russia could target its nuclear missile systems against Ukraine. This is what worries us," Putin said.
Ukraine said on Wednesday it was prepared to pass legislation barring the deployment of NATO military bases on its soil should it join the military alliance.
In mid-January, Yushchenko, Prime Minister Yulia Tymoshenko and parliamentary speaker Arseniy Yatsenyuk sent a letter to NATO Secretary General Jaap de Hoop Scheffer expressing their hope that the country could join an action plan for NATO membership.
Russia has been unnerved of late by NATO's ongoing expansion and Washington's plans to deploy missile defense bases in Central Europe, which the U.S. claims are needed to deter possible strikes from Iran and other "rogue states."