The ministry posted a statement on its website denouncing comments made by a U.S. State Department spokeswoman at a news conference Thursday, RIA Novosti reported.
"We view the declaration made by the official representative of the State Department, Victoria Nuland, that the United States will continue financing individual NGOs within Russia via intermediaries in third countries, bypassing Russian law, as open interference in our internal affairs," the statement said.
Nuland suggested Russian spot checks on NGOs to determine if any of their funding comes from the United States are "some kind of witch hunt." She said the department was providing money through third parties in other countries.
Agora, a Russian human rights organization, said this week the government has gone after 80 groups so far.