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Moscow's objections to the project, which includes participation by Romania, Poland, Turkey and Spain, "won't be the driving force in what we do," Ivo Daalder, the ambassador, told reporters at a breakfast session.
The US estimate of the Iranian ballistic missile threat has gone up, not down, over the two years since President Barack Obama opted for a new, four-phased deployment to protect the United States and NATO allies, Daalder said.
"It's accelerating," Daalder said of the US-perceived threat of Iran's ballistic missiles, "and becoming more severe than even we thought two years ago."
"We're deploying all four phases, in order to deal with that threat, whether Russia likes it or not," he added. At the same time, he urged Moscow to cooperate in both to deal with Iran and to see for itself that, as he put it, the system's capabilities pose its strategic deterrent force no threat.
If the perceived threat from Iran ebbs, "then maybe the system will be adapted to that lesser threat," Daalder said.
Obama pleased the Kremlin in September 2009 by scrapping his predecessor's plan for longer-range interceptor missiles in Poland and a radar installation in the Czech Republic, a move that helped to improve US-Russian ties.
But Moscow says that the revised version, using land- and sea-based Standard Missile-3 interceptors, could undermine its security if planned interceptor improvements become capable of neutralizing Russia's strategic nuclear deterrent force.
Washington and NATO have invited Russia to join in some aspects of the project, including possible joint early warning. Before agreeing to any such cooperation, Moscow is demanding a legally binding pledge from the United States that Moscow's nuclear forces would not be targeted by the system.
Russian President Dmitry Medvedev said on Wednesday that if the deadlock continues, Moscow would boost its early-waring radar to protect its nuclear missile sites, deploy weapons that could overcome a shield and potentially target missile defence installations to its south and west.
With NATO continuing largely to shrug off Russia's concerns, Moscow's ambassador to NATO, Dmitry Rogozin, was quoted as saying this week that Russia may review its cooperation with the supply route through Russia for NATO forces in Afghanistan.
Daalder said the sides remain at odds over, among other things, Russia's demand for the legally binding pledge, before any cooperation, that its nuclear forces would not be targeted by the NATO elements.
"They have gotten themselves quite hung up on our unwillingness to put this in legally binding writing," he said.
The administration was not convinced that such a pledge would be ratified by the US Senate, he said, nor should Moscow be convinced that even if it were, "we wouldn't necessarily at some point walk away from it," as the George W. Bush administration did from the 1972 Anti-Ballistic Missile Treaty, the only US-Russia missile defence pact.
That withdrawal opened the way for the creation of an anti-missile defence shield that the US government says is designed to protect the United States from countries like Iran and North Korea.
Daalder said that if the United States ever were placing interceptors to counter Russia's nuclear missiles, "we wouldn't deploy them in Europe. We would deploy them in the United States."
The physics of missile defence intercepts make it "easier and better to approach an incoming missile from the opposite side than it is to try to chase it down." he said. "That's the way that it works."