Secretary of State Condoleezza Rice signed the US-Czech deal in Prague
Russia has said it will be forced to react with military means if the US and Czech Republic go ahead with plans for a missile shield.
The statement came hours after the US signed an initial deal to base part of Washington's controversial missile defence system in the Czech Republic.
Moscow says siting the system near its borders could weaken its own defences.
It has previously threatened to aim its own missiles at any eventual base in Poland or the Czech Republic.
The deal, signed by US Secretary of State Condoleezza Rice in Prague on Tuesday, allows a tracking radar base to be set up on Czech territory.
The Pentagon says the shield is designed to counter a threat from the Middle East, not Russia.
'Not our choice'
The Russian foreign ministry statement said: "If a US strategic anti-missile shield starts to be deployed near our borders, we will be forced to react not in a diplomatic fashion but with military-technical means."
The plans are unpopular with many people in the Czech Republic
It said there was "no doubt that the grouping of elements of the strategic US arsenal faced towards Russian territory" would mean Moscow had to "take adequate measures to compensate for the threats to its national security".
"This is not our choice," it added.
The foreign ministry said it would continue to monitor developments but would remain open to constructive talks on issues of strategic stability.
The BBC's Adam Brookes in Washington cites Russia's ambassador to the UN as suggesting that the phrase "military-technical means" does not mean military action, but more likely a change in Russia's strategic posture, perhaps by redeploying its own missiles.
More likely still, our correspondent says, is that the Russians are trying to frighten the Czech parliament into backing out of the whole deal.
The next question, he says, is whether Poland will accept missile defence facilities as well, and how the Russians will respond to that.
The plans remain unpopular in the Czech Republic, while the US has failed to reach agreement with Poland on placing other parts of the system there.
The plans involve siting the tracking radar system in the Czech Republic and 10 interceptor missiles in Poland. The US wants the sites to be in operation by about 2012.
Czech opposition parties have strongly criticised the plans and are calling for a national referendum.
The plans will have to be approved by the Czech parliament, where the government would need the votes of the opposition parties to get them through.
Speaking after signing, Ms Rice said that the US and its allies faced "a growing missile threat that is getting ever longer and ever deeper" from Iran.
The Russian news agency Interfax earlier quoted a senior Russian official as saying the deal "complicates" global security.
In talks on Monday, US President George W Bush, attending his last G8 summit, and Russian President Dmitry Medvedev, attending his first, made little progress on the issue of the US missile defence system.