Merkel says the German government has demanded Russian authorities respect international standards of human rights.
Merkel's comments came in response to a plea from Germany's opposition Free Democrats for her to raise Khodorkovsky's case with Russian President Vladimir Putin. Her letter was released by the Free Democrats and published today in the "Berliner Zeitung" newspaper.
In the letter, Merkel says violations of human rights in the prison worry the German government greatly.
Khodorkovsky, the former chief of the now bankrupt oil giant Yukos, is serving an eight-year sentence for fraud in the Krasnokamensk prison colony.
Many observers believe he was arrested because he represented a political threat to President Vladimir Putin, a claim denied by the Kremlin.
Yukos was declared bankrupt by a Moscow commercial court on August 1.