Alexander Rumiantsev, making his comments after a series of terror attacks in Russia, said that the quantities stolen never amounted to more than tens of grammes.
"Over the past 25 years we have recorded several disappearances of military-quality nuclear material and it was always tens of grammes. These materials were always retrieved as a result of painstaking inquiries," he said.
He revealed however that only 10 percent of a 100 kilo quantity of natural uranium that also disappeared has been recovered.
But he added: "This substance could never be used to make nuclear weapons, something that the thieves surely ignored".
Rumiantsev reiterated that security measures were very tight at the country's nuclear power stations in the wake of the deadly attacks that included the downing of two planes, a suicide blast in Moscow and the Beslan hostage tragedy.
"It is clear that terrorists are planning to attack nuclear power stations, and this is why these are guarded by soldiers and interior ministry forces, who have very strict instructions over terrorist attacks," he said.
He also called for greater efforts to prevent the theft of radioactive isotopes used in industry and hospitals, something that happened "relatively frequently".