Russian Justice Minister Alexander Konovalov said earlier that, as of the end of May, four organizations had appealed to the ministry with pleas to be removed form the list.
The Center of Civil Analysis and Independent Research foundation (Center GRANI) and the Kostroma Center for Civic Initiatives Support were removed from the list following snap inspections of these organizations, a statement by the ministry said.
Commenting on the law, Russian President Vladimir Putin said it was aimed at limiting direct and indirect foreign interference and lobbying in the country.
Initially, the procedure for removing an organization from the list of "foreign agents," should it cease to receive funding from abroad, was not provided for in the law, lawmakers later amended the law to allow for such cases.