The move, with an amnesty for the two jailed members of the Pussy Riot punk band and the 30-member crew of a Greenpeace ship, appears designed to placate international critics of Russia’s rights record ahead of February’s Winter Olympics in Sochi.
Mr Putin waited until just after his tightly choreographed annual news conference to make the announcement, dropping the biggest news of the day after journalists had already peppered him with questions, including one about Khodorkovsky’s fate, in a four-hour marathon.
Mr Putin said that Khodorkovsky, who is set to be released in August 2014, had submitted an appeal for pardon, something he had refused to do before.
“He has spent more than 10 years behind bars. It’s a tough punishment,” Mr Putin said. “He’s citing humanitarian aspects – his mother is ill. A decree to pardon him will be signed in the nearest time.”
In October 2003, masked commandos stormed into his jet on the tarmac of a Siberian airport and arrested him at gunpoint. He was found guilty of tax evasion in 2005 and convicted of embezzlement in a second case in 2010.
Critics have dismissed the charges against Khodorkovsky as a Kremlin vendetta for challenging Mr Putin’s power.
In his Press conference, Mr Putin also confirmed that an amnesty approved by the Kremlin-controlled parliament on Wednesday will apply to the two members of Pussy Riot still in jail and the Greenpeace crew facing hooliganism charges for their protest at a Russian oil rig in the Arctic.
Asked whether he felt sorry for the two women, Mr Putin stood by his strong criticism of their irreverent protest at Moscow’s main cathedral, describing it as a publicity stunt that “crossed all barriers”.
He also alleged that the Greenpeace activists were trying to hurt Russia’s economic interests. He added that he did not mind that charges against the Greenpeace team were dropped under the amnesty bill, but that he hoped that “this will not happen again”.
Mr Putin weathered months of massive protests against his rule in 2011-2012, when more than 100,000 gathered to oppose his return to the Russian presidency. A demonstration in May 2012 a day before his inauguration for a third term ended in scuffles with police.
The amnesty bill included only eight out of 26 people tried or awaiting trial in connection with that protest. Two of them were freed in a courtroom as Mr Putin’s news conference continued.
Mr Putin defended the decision not to offer amnesty to others, saying that their release would give a bad example. “No one should be allowed to violently trample on the law,” he said.
Amid a strain in Russia-US ties, he also offered surprising support to President Barack Obama by saying that US National Security Agency surveillance is necessary to fight terrorism, but heres should be ground rules.
Mr Putin, a 16-year KGB veteran and the former chief of Russia’s main espionage agency, said that while the NSA programme “isn’t a cause for joy, it’s not a cause for repentance either”.
He argued that it was necessary to monitor large numbers of people to expose terrorist contacts. But “on political level, it’s necessary to limit the appetite of special services with certain rules”, he said.