Each team will receive about 45 million dollars over the next 18 months to develop prototypes that could prove the feasibility of such a defense.
"While this technology has been used by the US military and some foreign commercial airlines, the challenges in adapting these technologies for use commercially in the United States are significant," said Penrose Albright, assistant secretary for science and technology.
"In the US, with more than 400 airports and more than 6,000 aircraft in the commercial fleet, the maintenance cost of (counter-missile) technology at current system costs would be staggering."
The United States fears that terrorist groups, including Al-Qaeda, could use shoulder-fired missiles known as man portable air defense systems (MANPADS) to attack US airliners.
The devices, which include Soviet-built SAM7s and US Stinger missiles widely distributed among anti-Soviet Mujahadeen in Afghanistan in the 1980s, are small enough to pack into the trunk of an automobile and are widely available on the black market.
The missiles came to the world's attention with an attempt to shoot down an Israeli airliner shortly after takeoff from Mombasa two years ago. In November 2003, a cargo plane was hit by a missile shortly after taking off from Baghdad airport and had to make an emergency landing.