Gates said Russian initiatives such as a joint naval exercise with Venezuela in November posed little threat to the United States and he made light of Moscow's ageing military capabilities.
"I'm more concerned about Iranian meddling in the region than I am the Russians," Gates told the U.S. Senate's armed services committee.
"I'm concerned about the level of frankly subversive activity that the Iranians are carrying on in a number of places in Latin America," Gates said in response to a question from Sen. Mel Martinez, a Florida Republican.
"They're opening a lot of offices and a lot of fronts behind which they interfere in what is going on in some of these countries," Gates said, without elaborating.
Left-wing governments in Venezuela, Cuba, Ecuador, Nicaragua and Bolivia have all become allies of Iran in recent years, and other Latin American countries have diplomatic ties with the Islamic republic.
The United States is at loggerheads with Iran on a range of issues, above all Tehran's nuclear programme.
Iran says it only wants to generate power while the Washington and its allies accuse Tehran of trying to build a nuclear bomb, and former President George W. Bush branded Iran part of an "axis of evil".
President Barack Obama has promised dialogue with Tehran but Secretary of State Hillary Clinton suggested on Tuesday it may be up to the Iranians to make the first move.
Gates, who served as Pentagon chief for the last two years of the Bush administration and has stayed on under Obama, said he felt the best attitude to the visit of Russian warships to Venezuela was "nonchalance."
He said that if tensions with Moscow had not been high following the August war in Georgia, he would probably have tried to persuade Bush to invite the Russian ships to a port visit in Miami.
"I think they'd have had a lot better time than they did in Caracas," he said.
He also joked that pilots of Soviet-era Tu-160 "Blackjack" bombers should have been glad to have U.S. aircraft flying nearby as they made their way to Venezuela.
"When they complained about our escorting their Blackjack bombers to Venezuela, I wanted to say that we just wanted to be along there for search and rescue if they needed it," he said.
(Reporting by Andrew Gray; Editing by Kieran Murray)
