Germany's nuclear watchdog approved in September the shipment of 951 spent fuel elements originating from a research centre in ex-communist East Germany to the Mayak nuclear facility, 2,000 kilometres (1,200 miles) east of Moscow.
But Environment Minister Norbert Röttgen said Monday he had ordered the federal exports office to withhold its authorisation.
"The environment minister is not convinced there can be safe processing of the spent fuel elements at the Russian facility as required by law," a spokeswoman told a regular government press briefing.
Russia's Mayak facility in Ozersk, the planned destination for the waste, is a major nuclear reprocessing plant and was the site of a massive nuclear accident in 1957.
The fuel elements are currently at the temporary storage site Ahaus in western Germany. The spokeswoman said the waste would now remain there. The highly radioactive waste originally came from the Rossendorf research centre and was to be shipped in late 2010 or early 2011.
Rossendorf, in Dresden, was closed in 1991 and was one of the 20 research reactor plants set up across 17 countries in the former communist bloc. German environmentalists said they would stage protests against the shipment, which they branded "highly dangerous."
Demonstrators in Moscow rallied against the plans in August, citing the threat of "terrorist acts" and risk of forest fires leading to radioactive contamination.
A state of emergency was declared in Ozersk in August after Russia's wildfires blazed dangerously close to the plant.
A shipment of radioactive waste from France to Germany sparked mass protests last month.
Berlin has approved disputed plans to extend the life of the country's 17 nuclear power plants well beyond the planned shut-off date of around 2020.