Sergei Shoigu said that the U.S. had planned its surprise withdrawal from the intermediate-Range Nuclear Forces (INF) treaty long in advance, to counter Russia's and China's growing military clout.
Putin has also threatened to target European nations if they allow the U.S. to deploy new intermediate-range missiles.
"Strengthening Russia as an independent international player does not give rest to our NATO colleagues," Russian Defense Minister Sergei Shoigu said.
"This trend clearly indicates that NATO countries are trying in every possible way to prevent Russia from emerging as a geopolitical competitor."
"[The strategy] boils down to supporting any, even the wildest ideologies to weaken legitimate governments."
The S-500 struck a target 299 miles away.
Top U.S. military rivals Russia and China have pledged to deepen military ties and create a united front against the U.S. in its Syria and Iran policies.
People spotted a problem with Sergei Shoigu's claim about Russia's role in taking back territory from Islamist groups.
A Russian jet tried to intimidate a NATO jet while attempting to escort the Russian defense minister's plane in international airspace, state news agencies claim.