The decree (in Russian) accused the US of creating "a threat to strategic stability, as a result of unfriendly actions" towards Russia. So Russia had to take "urgent security measures".
Under the 2000 deal, each side is supposed to get rid of 34 tonnes of plutonium by burning it in reactors.
It is part of cuts to nuclear forces.
The US state department said the combined 68 tonnes of plutonium was "enough material for approximately 17,000 nuclear weapons". Both sides reconfirmed the deal in 2010.
'We fulfilled our duties'
But in April Mr Putin said the US was failing to fulfil its obligations to destroy plutonium. Instead, he argued, the US reprocessing method allowed plutonium to be extracted and used again in nuclear weapons.
Both sides had agreed to build special facilities for disposing of the surplus plutonium.
"We fulfilled out duties, we built that enterprise. But our American partners did not," Mr Putin said.
The US rejected that claim, insisting that its disposal method did not violate the agreement.
The Russian decree comes amid heightened tensions over Russia's bombing campaign in Syria, which some have described as a "war crime".
Russian planes are helping Syrian government forces to hit rebel groups, some of which are supported by the US and its Gulf Arab allies.
Russia is currently modernising its nuclear arsenal. The post-Cold War thaw ended in 2014 when the Russian military annexed Crimea from Ukraine. Russia says it is defending the legitimate interests of ethnic Russians in Ukraine.