Alexander Shprygin is among 20 Russian fans being deported.
They were detained on June 14 while traveling from Marseille to Lille to watch Russia vs. Slovakia.
Three other detained Russian fans have been jailed for up to two years over the violence in Marseille.
They are also banned from re-entering France for two years. The men received 12, 18 and 24 months in prison.
The arrests have angered Moscow, which summoned the French ambassador to protest.
A Russian foreign ministry statement warned against “further stoking of anti-Russian sentiments”.
Deputy foreign minister Arkady Dvorkovich was quoted by the Tass news agency as saying blacklists of troublemakers would be drawn up before the 2018 World Cup, which Russia is hosting.
Arkady Dvorkovich said those accused of violence in France may yet face trial in Russia.
“We need to figure out who did what,” he said.
Alexander Shprygin’s All-Russia Supporters Union is backed by the Kremlin. He is reported to hold far-right views and has been photographed giving a Nazi salute.
A statement from the union said Alexander Shprygin and the other 19 fans had been transferred to a deportation centre from which they will be expelled in the next five days.
It said the French authorities were taking the measures for “security reasons”.
Russia and England fans clashed before and after the two teams played on Saturday.
French police blamed 150 “well-trained” Russian hooligans for the violence.
Afterwards, Russia was hit with a fine and a suspended disqualification, meaning the team will be thrown out of the Euro tournament if their fans cause more trouble inside stadiums.
Five England fans were jailed for throwing bottles at police and a sixth jailed in connection with the violence.
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