The attack reportedly left three individuals with minor injuries.
Videos have appeared on social media showing fans being targeted at a restaurant in the city’s main square, although it has been reported that the incident was not between United and Villarreal supporters.
United confirmed that they are helping the victims of the attack, with three people reported to have suffered minor injuries.
The club said in a statement on Wednesday: “Club staff were assisting a number of United fans in Gdansk last night and today after an incident where some of our supporters were attacked outside a bar in the city.”
A total of 9,500 spectators will attend the game on Wednesday night, including 2,000 from each finalist. The majority of United fans are due to arrive in the city on the day of the game.
The Gdansk mayor, Aleksandra Dulkiewicz, condemned the attacks in a post on Twitter.
He said: “Yesterday there was a hooligan attack on the fans of the teams that came to the Europa League final. In Gdansk, an open and solidarity-based city, there is no place for any violence.
“Dear fans and guests, you are always welcome and we welcome you to our city!”