"Russian authorities used repressive laws on 'extremist organizations', 'foreign agents' and 'undesirable organizations' to reinforce a systemic crackdown on democracy, human rights and fundamental freedoms, and independent media," the statement reads.
"This has further deteriorated political pluralism in Russia and possibilities for the people of Russia to express their civil position freely."
The ministry also "regrets that the constraints, put by Russian authorities under the pretext of the epidemiological situation in the country, did not allow the participation of international observers from the Organization for Security and Co-operation in Europe (OSCE) in the elections".
"All these actions demonstrate Russia's distancing from democratic principles and cast a shadow of doubt on the transparency of the elections," it said.
The ruling United Russia party on Monday claimed a two-thirds majority in the State Duma. The opposition calls the elections fraudulent.
The parliamentary and local elections followed a crackdown on opposition figures, including jailed Kremlin critic Alexei Navalny.
With 85 percent of votes counted on Monday, United Russia was ahead with 49.76 percent of the vote, followed by the Communist Party with 19.61 percent.