"The family is coming today," spokeswoman Olga Pispanen told AFP. "They have not been together for 10 years."
Russia's most famous inmate flew to Berlin after walking free from a prison in northwestern Russia following a surprise pardon from President Vladimir Putin on Friday.
Khodorkovsky, who has said he would stay out of Russia, is mulling a move to Switzerland where his twin sons go to school and would like to discuss that plan with his family, the spokeswoman said.
Khodorkovsky's wife, twin sons and a daughter, who are all believed to be in Moscow, have reportedly had to sort out travel documents.
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On Thursday, Putin shocked Russia by announcing he would pardon Khodorkovsky, who was jailed for financial crimes in separate convictions in 2005 and 2010. He had been due for release in August 2014.
His supporters say the imprisonment was Putin's revenge against Khodorkovsky who financed the political opposition and openly criticised the Russian strongman.
His Yukos oil firm was broken up and sold off to the state.
On Saturday, Khodorkovsky reunited with his elderly parents, Marina and Boris, and his eldest son Pavel, his child from his first marriage.
Khodorkovsky said he would not seek revenge against Putin and pledged to help political prisoners held in Russian jails.