Russian Defence Minister Sergei Ivanov, who signed the protocol with US Secretary of State Condoleezza Rice on Thursday, said the deal did not limit or ban the trade of shoulder-launched weapons that had already caused problems in bilateral relations.
"The sides only undertake to keep partners informed of the sales, because only Russia and the United States produce these weapons," Ivanov said.
"The sides will do their best to encourage their allies and satellites to take steps against spreading portable anti-aircraft missile complexes."
Rice and Ivanov are in the Slovak capital Bratislava as part of the delegations for a meeting between US President George Bush and Russian President Vladimir Putin.
"It serves as an example of what the United States and Russia can accomplish together on such vital issues," a US State Department fact sheet said.
"We're going to work with the Russians to decrease stockpiles of MANPADS"
Portable anti-aircraft missile complexes, also known as MANPADS, do not need a launching pad and are easy to fire and disguise, making them attractive to armed groups fighting governments around the world.
The US State Department said in a statement that about one million such devices have been produced worldwide, with a much smaller number, probably numbering in the thousands currently in the hands of "non-state actors".
"We're going to work with the Russians to decrease stockpiles of MANPADS," a senior Bush administration official said in Bratislava after the agreement was signed.