Since at least 2015, the group created thousands of false social media profiles and email accounts that appeared to be from people inside the US and were aimed to "create and amplify divisive social and political content", including on significant current events, such as deadly shootings in SC and Las Vegas, prosecutors said in court papers.
Prosecutors said that since 2014, Khusyainova has been handling the finances for Project Lakhta operations to sow divisiveness and confusion in United States elections.
America's justice department disclosed the latest criminal complaint soon after U.S. intelligence agencies said they were concerned about efforts by Russia, Chinaand Iran to influence U.S. voters and policy.
Those companies have been indicted in a separate case by special counsel Robert Mueller for allegedly taking part in the massive Russian campaign to interfere in the 2016 presidential election.
Those allegedly involved in the operation attempted to present themselves as Americans, the DOJ said.
The social media efforts specifically focused on the shootings of church members in Charleston, South Carolina, and concert attendees in Las Vegas, Nevada, the Charlottesville "Unite the Right" rally, which left one counterprotester dead, and police shootings of African-American men, the complaint says.
"Prigozhin, who was among those personally charged by Mueller, has been dubbed "[Vladimir] Putin's cook" by Russian media because his catering business has organised banquets for Russia's president and other senior political figures. They were also told to say that McCain had a "pathological hatred toward Donald Trump and toward all his initiatives".
"Today's charges allege that Russian national Yelena Alexeyevna Khusyainova conspired with others who were part of a Russian influence campaign to interfere with United States democracy", said Assistant Attorney General John Demers.
The indictment was released as the head of the USA intelligence community issued an official warning of interference by China, Iran, and Russian Federation in the upcoming election in a possible reprise of the Moscow-tainted presidential campaign of 2016.
The two-page statement about foreign influence was issued just weeks before the November 6 elections by the Office of the Department of National Intelligence, the Justice Department, the Federal Bureau of Investigation and the Department of Homeland Security. They also distribute propaganda and plant disinformation against political candidates, the departments said.
"The strategic goal of this alleged conspiracy, which continues to this day, is to sow discord in the US political system and to undermine faith in our democratic institutions", US Attorney Zachary Terwilliger said in a statement.
"Currently, we do not have any evidence of a compromise or disruption of infrastructure that would enable adversaries to prevent voting, change vote counts or disrupt our ability to tally votes in the midterm elections".
But they said, "Some state and local governments have reported attempts to access their networks, which often include online voter registration databases, using tactics that are available to state and nonstate cyber actors".
China has denied that it is interfering in United States affairs.