A sign directed at Bolton striker Marvin Sordell, who was racially abused by one of the club's fans last month, was unveiled at The Den during the Lions' 2-1 win against Derby in the Championship on Saturday.
The banner, which read "Sordell is a c***", related to complaints made by Sordell after he was abused by fans while warming up for a match on October 6, leading to a 13-year-old boy being banned from Millwall's ground.
A Metropolitan Police spokesman said six men were arrested on suspicion of public order offences, and have been bailed until early December.
The banner on display was swiftly removed by Millwall staff.
The club has so far refused to comment on the issue, and assistant manager Joe Gallen - standing in for Lions manager Kenny Jackett, who missed the game with flu - also opted not to discuss the matter.
Sordell, a member of Britain's squad at the Olympic Games this summer, tweeted after Bolton played there, that his team-mates Lee Chung-young, Darren Pratley and Benik Afobe were all subjected to racist taunts at the New Den.
Last week Millwall confirmed the 13-year-old had admitted abusing Sordell and subsequently issued a written apology, which the player accepted.
Millwall decided not to impose a life ban on the teenager but offered him a place on an educational programme instead.
Sordell also faced racist abuse from Serbia fans while playing for England Under-21s in Krusevac on October 16.