Alexander Torshin, the head of Russia's central bank, and Butima met with Donald Trump, Jr.at the NRA's 2016 convention.
Several years later, in August 2016, Butina entered the United States on a student visa while working as a special assistant to a high-level official in the Russian government.
Butina did not speak during the brief hearing other than to state her name.
The agency said Butina, 29, who lives in Washington, D.C., acted as an agent inside the U.S.
Maria Butina was arrested Sunday on a charge of conspiracy to act as an unregistered agent of the Russian government.
Neither the political party, nor the gun rights organization are specifically named in this complaint, although analysts have speculated that, judging from context from the entire document (and Butina's known history), the gun rights organization is the NRA.
The affidavit also contains apparent communications, by direct message on Twitter, between Butina and the unnamed Russian official.
The charges were drawn up by Special Counsel Robert Mueller, the former Federal Bureau of Investigation director who is looking into Russian interference in the November 2016 vote and whether any members of Trump's campaign team colluded with Moscow.
Ms Butina is a Russian gun rights advocate who founded a pro-gun organisation, the Right to Bear Arms, in that country in 2011.
Trump on Monday again denied any collusion between his campaign and the Kremlin and appeared to accept Russian denials of any meddling in U.S. elections following his summit with Putin.
"The (GUN RIGHTS ORGANIZATION) [is] the largest sponsor of the election to the U.S. congress", read the indictment.
Butina hosted several leading NRA executives and pro-gun conservatives at her group's annual meeting in 2015, according to those reports.
The charges against Butina come days after the Justice Department unveiled an indictment against 12 Russian intelligence officers for allegedly conspiring to hack Democrats in 2016 and just hours after President Trump cast doubt on Russia's involvement in an extraordinary joint news conference with President Putin.
The New York Times posted the entire affidavit filed against Butina online. In February 2017, the Daily Beast reported that she was close to Republican activist Paul Erickson, who appeared at her birthday party months earlier dressed as Rasputin.
Torshin said in 2011 that he was a "life member" of the NRA along with Butina whose stated goal was to further the right to private firearms ownership in Russian Federation.