For Human Rights director Lev Ponomaryov said Thursday's ruling was a "suspension of the organization's activities," a phrase that means the NGO would have to completely close, RIA Novosti reported.
The only legal restriction imposed on the NGO is a ban on organizing rallies and demonstrations, Russian media outlets said.
Ponomaryov said Justice Ministry inspectors found some minor irregularities in the organization's paperwork, including its charter.
"We explained that we are surely ready to make the corrections they want. But the charter can be amended only during the [organization's] congress, held every three years. The last congress was in fall 2012," he said. "We have a normal dialogue with the Justice Ministry, and I'm not sure they're acting on someone's orders. I think we'll be able to find common ground."
For Human Rights was one of hundreds of non-government organizations that came under increased government scrutiny after Russian lawmakers passed a controversial law in 2012 that required NGOs funded from abroad and engaged in "political" activities to register as "foreign agents," a term critics say is akin to "spy."
Ponomaryov told media the suspension has nothing to do with the controversial law.