"Our experts believe the system threatens our national security," Putin said at his final annual news conference in the Kremlin. "If it appears, we will be forced to respond appropriately - we will have to retarget part of our systems against those missiles."
He also said Russia could be forced to redirect its missiles at Ukraine if NATO bases are deployed in the country.
"We will be compelled to aim our missiles at facilities that we consider a threat to our national security, and I am putting this plainly now so that the blame for this is not shifted later," Putin said.
However, he stressed that Russia did not intend to "retarget anything at anyone without extreme necessity."
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.
On Tuesday, Putin said Ukraine's moves to join NATO were its internal affair, but went on to say that, "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."
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 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."
Moscow said it possesses the relatively inexpensive technical capability which would offer an appropriate response to U.S. missile defense deployment in Europe.
The U.S. administration is planning to construct a base for 10 two-stage missile interceptors in Poland, modify its X-band radar on the Kwajalein Atoll in the Pacific and relocate it to the Czech Republic, and to deploy a new forward-based radar to an unspecified location.
The 2008-2013 budget for the project is estimated at about $4.8 billion.
In his 2008 FY Budget proposal, Bush asked Congress to approve the allocation of $310 million for the deployment of U.S. missile defenses in Europe, but lawmakers cut the amount by 27% to $225 million.