"In Russia's relations with Nato there are several issues on which we have not found common positions. This above all concerns the CFE treaty and missile defence," Serdyukov said.
The Russian official also said that Washington was "beginning to better understand our concerns".
The comments came after Robert Gates, the US defence secretary, outlined proposals on Tuesday to let "a Russian presence" monitor a missile defence radar facility that Washington hopes to build in the Czech Republic.
The radar is part of a proposed missile defence system that would also comprise a small number of interceptor missiles in Poland.
The US government insists that the system is not directed against Russia but against "rogue states".
But Russia has said that the US plan threatens its security.
Serdyukov also said that the Russian threat to withdraw from the CFE treaty "is stimulating Nato countries to take a decision as soon as possible" on a demand by Russia, that an updated version of the treaty be ratified.
Nato countries have said they would only ratify a revised version of the CFE treaty once Moscow has lived up to a pledge made in 1999 to pull its troops out of the former Soviet republics of Georgia and Moldova.