"It's impossible to do anything about those 10 days he spent there, but it will be removed from his legal documents," a spokesman for a support group - "Press-centre Mikhail Khodorkovsky" - which monitors his life in jail, told Reuters news agency.
A local court had previously ruled that Khodorkovsky, once estimated to be Russia's richest man, had been treated unfairly when he was reprimanded for leaving his place in the prison's sewing workshop without asking permission.
Khodorkovsky, known for his political ambitions, says he is a victim of a Kremlin political campaign.
He was once-estimated to have a $15bn fortune and has been in jail since October 2003, after Russian special forces stormed his private plane at a Siberian airport.
The Kremlin denies that there is any political motivation behind his treatment.