Once Russia’s richest man, the 50-year-old looked pale and thin but happy in a photograph of him being greeted by German well-wishers yesterday after landing in a private jet.
President Putin, who surprised Russians by announcing Mr Khodorkovsky’s pardon on Thursday, said he was acting out of “principles of humanity”.
A Russian government source said freeing his best-known and potentially most powerful critic could deflect international complaints about Mr Putin’s human rights record as Russia prepares to host the Winter Olympics at Sochi in seven weeks.
The move, which Putin said was prompted by the illness of Mr Khodorkovsky’s mother, also appeared to show that Mr Putin is feeling confident in his control of the country after facing down street protests when he was re-elected last year.
Within hours of being released from Penal Colony No 7 at Segezha, deep in the sub-Arctic forest near the Finnish border, Mr Khodorkovsky was in the German capital and issued a statement confirming that he had sought a pardon for family reasons and had not admitted guilt on the fraud charges.
“I appealed to the Russian president on 12 November with a request for a pardon in connection with family circumstances,” he said. “The issue of an admission of guilt was not raised.
“I am very eager for the moment when I can hug my loved ones,” he said.
His mother Marina, 79, said by telephone from Moscow: “I want to just hug him. I don’t even know yet what I am going to say to him.”
Her son said last month that she was facing a second bout of cancer and he might not see her again.
“My father is free and safely in Germany,” his son, Pavel Khodorkovsky, said on Twitter. “Thank you all for the support you’ve given my family over these years.”
The former oil baron had been due to be released next August but supporters feared the sentence could be extended, as it was before. He spent the last few years working at the jail, in an area once part of Soviet leader Josef Stalin’s Gulag labour camp system.
In flying to Germany and possibly into exile, Mr Khodorkovsky, named a “prisoner of conscience” by Amnesty International, was following a route taken by Soviet-era dissidents such as Gulag Archipelago author Alexander Solzhenitsyn, who was expelled to West Germany 40 years ago.
Mr Khodorkovsky fell out with Mr Putin before his arrest in 2003 as the president clipped the wings of “oligarchs” who had become powerful during the chaotic years of Boris Yeltsin’s rule following the collapse of Soviet communism.
His company, Yukos, was sold off, mainly into state hands, following his arrest at gunpoint on an airport runway in Siberia on fraud and tax evasion charges.