Russian prison officials said Mr Khodorkovsky had requested travel papers to see his sick mother there.
Mr Khodorkovsky’s father told AP he and his wife were still in Moscow but were planning to fly to Germany, where she has been treated in the past.
Mr Putin earlier said he had signed the pardon on “the principles of humanity”.
Mr Khodorkovsky, 50, had been in custody for a decade.
‘Personal request’Mr Khodorkovsky left the penal colony where he was being held, in the Karelia region of north-western Russia, early on Friday afternoon.
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