The Federal Registration Service at the Justice Ministry says the Center has failed to provide information about its activities over for the past five years.
It has now filed a suit with a Moscow city court asking for the Center to be closed down.
The Research Center's director, Lyubov Vinogradova, told RFE/RL's Russian Service that the Ministry's claims were groundless.
The Research Center for Human Rights was set up in 1992. It groups several human rights organizations, including the Moscow Helsinki Group and the Union of Committees of Soldiers' Mothers.