"The troops are being moved onto trains and military transport aircraft. This will take around 20 days," General Valery Gerasimov, Russia's chief of general staff, was quoted as saying by RIA Novosti news agency.
He dismissed a journalist's suggestion that the pull-out would be completed by June 1.
Putin on May 19 called an end to military exercises in regions bordering Ukraine, where troops had been deployed since March.
NATO chief Anders Fogh Rasmussen said Thursday that limited Russian troop movements near the border with Ukraine "may suggest" preparations for a withdrawal.
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Gerasimov insisted that the troops did not present a threat to Ukraine.
"The subject of a Russian threat has been actively repeated by Ukrainian media recently simply to scare the public," he said.
The deployment of an estimated 40,000 troops raised fears that Moscow would intervene in eastern Ukraine to back pro-Russian separatists. Russia has insisted the exercises were routine.
"The lack of destabilising gatherings of troops close to the Ukrainian border was confirmed by more than 10 inspector groups coming from NATO countries and Ukraine, which we accepted on our territory," he said.