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," 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 Putin's power.
In his press conference, 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, 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 Wednesday's amnesty bill, but that he hoped that "this will not happen again."
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 8 out of 26 people tried or awaiting trial in connection with that protest. Two of them were freed in a courtroom as Putin's news conference was still ongoing.
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," Putin said.
Amid a strain in Russia-U.S. ties, he also offered surprising support to President Barack Obama by saying that U.S. National Security Agency surveillance is necessary to fight terrorism. The government should "limit the appetite" of the agency with a clear set of ground rules, he said.
Putin, a 16-year KGB veteran and the former chief of Russia's main espionage agency, said that while the NSA program "isn't a cause for joy, it's not a cause for repentance either" because it is needed to fight terrorism.
He argued that it's 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.
Putin added that the efficiency of the effort and its damage to privacy is limited by the sheer inability to process such a huge amount of data.
Asked about former NSA contractor Edward Snowden, whom Russia has granted asylum, Putin insisted that Moscow isn't controlling him.
He argued that any revelations published by Snowden must have come from materials he provided before landing in Russia, and reaffirmed that Moscow made providing refuge to Snowden conditional on his halting what he called ant-American activities.
Putin said he hasn't met with Snowden. He insisted that Russian security agencies haven't worked with him and have not asked him any questions related to NSA activities against Russia.
Putin also dismissed a report claiming that Moscow stationed its state-of-the art Iskander missiles in its Kaliningrad exclave region that borders NATO and EU members Poland and Lithuania, but added that he continues to consider such a move a possible way of countering the U.S.-led missile defense system in Europe.
Both Poland and Lithuania have expressed concern about such a possibility, and Washington warned Moscow against making destabilizing moves. Putin said Russia has long considered it, but added that "we haven't made the decision yet" on deploying them.
The Kremlin sees Putin's annual press conference as key in burnishing Putin's father-of-the nation image.
Journalists waved handwritten posters with names of their cities to attract Putin's eye, and one succeeded by holding up a Yeti doll in a T-shirt with the name of her region. One journalist invited Putin to attend a party at her newspaper.
Many acted as envoys for their towns or provinces, asking for subsidies or state support for specific projects. Others complained about official abuses or asked for his personal patronage.
One journalist from the far east complained about a clash between the local police and drug enforcement agency. Putin ordered an immediate check. An inspection team headed to the region before the news conference was over.