Rasmussen was speaking at NATO headquarters in Brussels, where discussions over the defense shield were held between foreign ministers from the 28-member alliance, including U.S. Secretary of State Hillary Clinton and Russian Foreign Minister Sergei Lavrov.
Rasmussen said NATO's proposed defense shield will protect Europe from missiles fired from rogue nations and would not "threaten" Russia or its strategic position in the region.
"Within NATO, we are making good progress in developing an integrated, alliance-wide missile defense system," Rasmussen said. "This system does not threaten Russia. Nor does it alter the strategic balance. So I am confident that there, too, we can find a way forward, in a spirit of dialogue, trust, and transparency that we have built up around this table over the last 15 years."
He reiterated the alliance’s commitment to working closely with Russia despite making little progress on the issue so far.
"It is well-known that we do not agree on all issues," Rasmussen said. "But it is also clear that we are committed to continue discussing all issues, at all times -- because the NATO-Russia Council is an all-weather forum. And it still has untapped potential."
Russia, meanwhile, has long suspected the missile-defense shield will neutralize its nuclear deterrent.
Russia has previously demanded “legally binding” guarantees that it will not be targeted, since the shield could reach parts of its territory.
According to some reports, NATO is expected to declare the missile defense shield, a U.S.-sponsored project, partially operational at a NATO summit in Chicago in May, although full capability is not expected before 2020.
Romania has already signed a deal with NATO for 24 interceptor missiles to be based there, while Turkey has agreed to have in its territory a sophisticated American radar system.
At the meeting, NATO and Russian ministers also discussed a plan to give the alliance a new logistics facility on Russian territory for the transfer of military cargo to and from Afghanistan.
Moscow has provided NATO with air and railway routes for carrying supplies to and from the landlocked country.
The supply route has become particularly important since Pakistan blocked NATO supplies from crossing its territory last November.
The move comes despite Lavrov criticizing NATO for what he called its "artificial" timeline for withdrawal from Afghanistan.
"We are very concerned about how events will unfold after the planned withdrawal of the International Security Assistance Force (ISAF) from Afghanistan," Lavrov said. "We believe any withdrawal must be synchronized with the process of ensuring that Afghan security forces are capable of controlling the situation in their own country and combating extremist groups and drug traffickers."
The majority of the NATO-led international force is scheduled to leave Afghanistan by 2014. NATO has said it is planning to train some 350,000 Afghan soldiers and policemen by the end of this year as it works to fill the void that will be created by the withdrawal of foreign combat troops.