Anatoly Serdyukov met with NATO defense chiefs in Brussels at a Russia-NATO Council session.
"Our relations with our NATO partners are highly valued. But there are issues on which we cannot find agreement. These are the CFE treaty and missile defense," Serdyukov told reporters after the meeting.
"None of this is helping efforts to improve transparency and trust in our cooperation, and puts obstacles in the way of moving cooperation to a new level."
Russia staunchly opposes U.S. plans to place 10 interceptor missiles in Poland and a radar station in the neighboring Czech Republic.
NATO members' reluctance to approve an amended Cold War-era Conventional Forces in Europe (CFE) treaty has also proved a source of tension. Russia imposed a moratorium on the treaty late last year.
