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The Football Association is investigating tweets of an alleged racist and Islamophobic nature which appeared on the account of Millwall's head of youth recruitment Barry Dunn.
The numerous offending tweets, which have been seen by BBC Sport, were on an account which had Dunn's name on it.
The Twitter account now appears to have been deleted.
In a statement to BBC Sport, Millwall said they are "co-operating fully with the governing body".
A spokesperson for the Championship club added: "The club is aware of an active FA investigation into the social media activity of a staff member.
"The club cannot comment further while the investigation is ongoing but wishes to reiterate its zero-tolerance policy against discrimination of any kind."
In March, Millwall signed the Muslim athlete charter, pledging to "actively support players" of the Islamic faith.
At the time, the club had seven Muslim players in their academy and chief executive Steve Kavanagh said of signing the charter: "It is imperative the club incorporates the differing needs of our Muslim players."
He added: "As a club we are striving to create an environment where players and staff can maximise their ability and talent and this will help those of Muslim faith to do exactly that."
