The move comes as Moscow is seeking to advance talks over the placement of Glonass stations in the US, Xinhua reported.
"We have worked out and implemented measures that exclude the use of these stations for military purposes. Now they are under our full control," Rogozin tweeted.
Roscosmos, the Russian Federal Space Agency, confirmed the measures would be implemented from Sunday.
Rogozin also said that Moscow has initiated talks with the US on the deployment of Glonass stations on the US territory. The talks are expected to last until Aug 31, and "new decisions will be made" afterwards.
Rogozin warned earlier this week that Russia would stop the operations of these GPS stations June 1 and might start dismantling them from Sep 1 as a response to Washington's anti-Russia sanctions and its refusal to plant Glonass ground base stations on the US territory.
Glonass is the Russian equivalent of GPS, designed for military and civilian use.