Russian President Dmitry Medvedev promised to shut the reactor
Russia has shut down its last weapons-grade plutonium reactor.
The move came after a pledge this week from Russian President Dmitry Medvedev at a 47-nation nuclear security summit in Washington.
Plant bosses pressed the red "stop" button to commence decommissioning process at 0400, the official Russian news agency reported.
The ADE-2 reactor opened in 1964 in Zheleznogorsk, then a secret city known as Krasnoyarsk-26.
Some 2,500 miles east of Moscow, the military production complex was founded in 1950 on the orders of Joseph Stalin.
Two other reactors there were closed in 1992, said Yelena Golovinkina, spokeswoman for the Mining-Chemical Complex, which houses the reactor.
Russia's defence ministry stopped using the plutonium for military needs in 1995, and the plant was used mainly to heat the city of Zheleznogorsk, she added.
The closure of the reactor came after Mr Obama and Mr Medvedev signed a nuclear disarmament treaty, described by both sides as a major step towards improving strained US-Russian relations.
The powers pledged to dispose of 34 tons of excess weapons-grade plutonium each, enough to make 17,000 weapons.
The cost of disposing of the Russian plutonium would be $2.5bn, Russian Foreign Minister Sergei Lavrov estimated. The US will contribute $400m to the Russian disposal.
The US president hailed the move by his Russian counterpart after Tuesday's summit.
"This important step forward continues to demonstrate Russia's leadership on nuclear security issues, and will add momentum to our shared global effort," Mr Obama said.