The German Foreign Ministry said Khodorkovsky was in the country as a private citizen, the New York Times reported. A Russian official said he requested documents allowing him to go to Germany to visit his mother while she was undergoing medical treatment, although the Times reported Marina Khodorkovsky was in Moscow.
Earlier, Khodorkovsky's lawyer confirmed his release. The Kremlin said the pardon was granted on humanitarian grounds, RIA Novosti reported.
Khodorkovsky, the founder of Yukos Oil and once said to be the richest man in Russia, was arrested in 2003 and sentenced to nine years in prison on embezzlement and tax evasion charges. His prison term was extended in 2010 after he was found guilty of a large-scale theft of oil and money laundering.
Russian prosecutors had recently said they were preparing a third case against him, the Times said.
Khodorkovsky had been serving out his prison sentence, which was to end in August 2014, in a penal facility near Segezha, close to Russia's border with Finland.
Putin announced the decision to pardon Khodorkovsky following a 4-hour question-and-answer session with Russian and foreign journalists Thursday.
Putin said Khodorkovsky had served a long sentence for a serious crime. He cited Khodorkovsky's mother's illness as a reason for granting the pardon request.
"[Khodorkovsky] cites humanitarian reasons," Putin said of the pardon application. "In line with the law, Mikhail Borisovich [Khodorkovsky] should have signed the necessary document [requesting a pardon], which he didn't do. But recently he signed this document, and it was addressed to me with an appeal for clemency."
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