A group of Everton fans were attacked by around 50 hooligans at a bar in Lille ahead of Thursday's Europa League match between the two clubs.
Eyewitness reports suggested the supporters were attacked with metal chairs and then sprayed with CS gas as police attempted to deal with the disorder on Wednesday night.
In a statement, Everton said two fans had suffered minor facial injuries and been taken to hospital.
The incident happened at the Australian Bar, where a group of fans had spent the afternoon and evening.
The Everton statement read: "The club has been made aware of an isolated incident in a bar in Lille on Wednesday evening in which a number of Evertonians were attacked by a group of around 50 local men.
"The club understands that two Everton fans suffered minor facial injuries and were taken to the local hospital, and that this was the only incident in what was otherwise a good-natured evening in the city centre.
"The club are in continual contact with Merseyside police officers, who are in Lille today, and the city's police representatives."
ESPN FC's Everton blogger Luke O'Farrell, who was at the Australian Bar, reported that the day had passed without trouble until the incident on Wednesday evening.
He tweeted: "In the Aussie bar all night. Full of Blues singing, no sign of trouble. Group of EFC fans suddenly burst inside to get away from Lille fans.
In the Aussie bar all night. Full of Blues singing, no sign of trouble. Group of EFC fans suddenly burst inside to get away from Lille fans.
- Luke O'Farrell (@lukeofarrell) October 22, 2014
"All hell breaks loose -- still no sign of police. Police finally turn up, spray EFC fans, assemble outside the bar, blocking EFC fans off.
"One EFC fan questioned police approach. Greeted with a truncheon and a police dog, which only underlined their shoddy, heavy-handed efforts.
"[Now] Back at hotel. Reactions to events spoke volumes. Bar staff helping sprayed fans; other Lille fans easing tensions, against police approach."
Greg O'Keeffe, the Liverpool Echo's Everton correspondent, spoke to a doorman at the bar, who claimed the attack happened when a group of local hooligans charged at the Everton fans from a side street.
O'Keeffe reported: "Everton fans were enjoying themselves and it had been peaceful, with kids playing football all afternoon.
"The doorman of the Australian bar told me that at around 10.30pm up to 100 hooded Lille hooligans swarmed from a side street and attacked Everton fans smoking outside and it was totally unprovoked.
"Lille thugs used metal chairs to batter fans outside and tried to smash their way into the pub to attack those inside. Local police were on scene within minutes and indiscriminately used gas on EFC fans asking for help."