The Football Association is investigating tweets of an allegedly racist and Islamophobic nature that appeared on the account of Millwall youth recruitment manager Barry Dunn.
The numerous offensive tweets, which were seen by BBC Sport, were on an account that bore Dunn’s name.
The Twitter account now appears to have been deleted.
In a statement to BBC Sport, Millwall said they are “fully cooperating with the governing body”.
A spokesman for the Championship club added: “The club is aware of an active investigation by the FA into the social media activity of a member of staff.
“The club cannot comment further while the investigation is ongoing but would like to reiterate their zero tolerance policy against any form of discrimination.”
In March, Millwall signed the charter of the Muslim athlete, pledging to “actively support actors” of the Islamic faith.
At the time, the club had seven Muslim players in its academy and chief executive Steve Kavanagh said of the charter signing: “It is imperative that the club incorporates the different needs of our Muslim players.”
He added: “As a club, we strive to create an environment where players and staff can maximize their abilities and talent, which will help Muslims do just that.”