Putin revealed after his marathon annual news conference that Khodorkovsky had for the first time written a request for a pardon, citing humanitarian circumstances as his mother is ill.
Khodorkovsky's legal team said it had no information that the former head of the now defunct Yukos oil giant had asked for a pardon but the Kremlin said the request had been personally signed by him.
"I think given the circumstances we can take the decision and very soon the decree to pardon him will be signed," Putin said in comments broadcast by state television.
The Russian leader said the 50-year-old Khodorkovsky -- who was convicted of fraud and embezzlement -- had not done this until now.
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"He did not do this and then quite recently he wrote such a document and addressed me with a request for a pardon," said Putin while referring to Khodorkovsky with the respectful patronymic form as Mikhail Borisovich.
"He has already been in detention more than 10 years, this is a serious punishment and he is referring to humanitarian circumstances as his mother is ill," said Putin.
"We do not have such information although there were requests to pardon him over the years from different individuals."
Kremlin spokesman Dmitry Peskov however told AFP that the request had been personally "signed" by Khodorkovsky.
Khodorkovsky first became the darling of Western investors nearly 15 years ago when he turned his Yukos oil company into one of the country's most transparent firms.
He used his vast fortune -- estimated at one point at nearly USD 20 billion -- on efforts to prop up both the liberal and communist opposition to Putin in parliament prior to his 2003 arrest.
Khodorkovsky was snatched off his corporate jet by special security forces in October 2003 shortly after Putin warned tycoons who disagreed with government policies about possible probes being launched into their wealth.