The entire international system of arms control would be jeopardised if the project continued, he warned, as it would contravene the 1972 Anti-Ballistic Missile (ABM) treaty.
Mr Putin, speaking during a historic live webcast on BBC News Online, said US insistence on the missile programme would jeopardise the entire international system of arms control.
The event, carried live on BBC News Online, was conducted from inside the Kremlin. A relaxed-looking Mr Putin revealed aspects of his private life, as well as dealing with major political issues.
Mr Putin's comments on Star Wars came as he answered a question from a News Online reader in Australia, who asked what Russia's response would be if the US pressed ahead with its anti-missile defensive shield.
The entire international system of arms control would be jeopardised if the project continued, he warned, as it would contravene the 1972 Anti-Ballistic Missile (ABM) treaty.
Russia's ratification of the Start II treaty was based on the ABM treaty, Mr Putin said, and if one ceased to operate, the other would too.
The president insisted that he wanted to work with Europe and the US to determine the nature of the threat from the "rogue" states, and to overcome it together.
But asked about his personal relationship with President Bush, Mr Putin said he did not foresee any particular problems, and he hoped that "common sense" would prevail.
Mr Putin also faced questions over his policies in Chechnya, where Russian forces have been accused of committing atrocities in the course of putting down a separatist rebellion.
"The Russian Army was forced to rebut a challenge by international terrorists," he said, adding that some Chechens supported Russian policy.
Mr Putin said the webcast gave him the chance to deal with a "lack of understanding" in the west over what was happening in the Caucasus and Chechnya.
Asked about freedom of speech, he said Russia was democratic and would remain so, and reassured the reader who raised the question that freedom of speech was safe.
Media barons who had illegally privatised state assets, including media outlets, would be obliged to obey the law, he said - but Russia would not crush democratic institutions, or act outside the law.
The questions from BBC News Online readers were put to President Putin by correspondent Bridget Kendall. She and two Russian journalists, all armed with laptop computers, selected questions in turn.
Mr Putin also gave details of his daily routine - revealing that he exercises daily, loves Russian literature and popular classical music, and used to like French films.
The forum began with a question about the president's own internet use. Mr Putin said the internet was a "very promising" form of communication - but admitted he was a lazy user who left most of his surfing to his advisers.
He also announced a contest to revamp his presidential website, after a question from a Russian reader who complained about its current state.
Bridget Kendall says agreeing to the interview was something of a gamble for Kremlin aides, but they saw it as a chance to boost Mr Putin's image and show off Russia's hi-tech skills.