French authorities announced the deportation order on Thursday, two days after prosecutors in Marseille stopped a bus full of Russian football fans following clashes with England supporters during the opening days of Euro 2016.
The leader of the "All-Russia Supporters Union," Alexander Shprygin, who was among the 20 fans to be deported on Thursday, had previously been photographed giving a Nazi salute.
The supporters' association is also backed by Russian President Vladimir Putin.
In response to Tuesday's arrests, the Russian Foreign Ministry summoned the French Ambassador, Jean-Maurice Ripert, calling the detentions "unjustifiable."
"We cannot turn a blind eye to the fact that [the French] are trying to ignore the absolutely provocative actions of fans from other countries," Russian Foreign Minister Sergei Lavrov said.
The ministry warned that "further stoking of anti-Russian sentiments ... could significantly aggravate the atmosphere in Russian-French relations."
After three days of violence between fans on the streets of Marseille, fresh clashes had erupted on Saturday night in the city's Stade Velodrome stadium after a large group of Russian fans stormed the England stands, minutes after the match ended 1-1.
England supporters were seen jumping over high fences to escape the group of Russians as they charged into the rival section, throwing objects, tearing down flags and seemingly attacking anyone in their path.
In response to the violence, Russia was handed a final warning from European football association UEFA. Russia now faces expulsion from the tournament in the event of more fan violence during matches. England has also been warned.
Three hundred arrests during Euro 2016
UEFA's powers to punish fan misbehavior stop at the stadium turnstiles. Outside the stadium hooliganism becomes a police matter.
French authorities jailed five England fans for throwing bottles at police, while a sixth was also imprisoned in connection to last weekend's violence.
According to the French Interior Ministry, of the 300 people arrested since the Euro 2016 tournament began last Friday, "196 were taken into custody, eight convicted to jail terms and three handed suspended sentences."