The foundation is also accused of "actively supporting fake patriots and members of banned terrorist and extremist groups", reports the news agency AFP.
The announcement comes after the foundation, together with several other non-governmental organizations, in July submitted a case to the UN Committee on Human Rights, where Russia is accused of human rights violations in Ukraine.
Earlier this summer, among others, the independent newspaper The Moscow Times and the German Konrad Adenauer Foundation, which works on democracy issues, were labeled as "undesirable" by Russia's Prosecutor General.
The label means that the organizations are forced to terminate their activities in Russia, and that Russians who collaborate with or finance them can be prosecuted.