The banner was unveiled in a Millwall section of the Lion's New Den ground during their 2-1 win against Derby on Saturday.
It related to Bolton striker Marvin Sordell, who was abused by fans while warming up for his side's game at the East London team's stadium on October 6, leading to a 13-year-old boy being banned from the ground.
Sordell, 21, who represented Great Britain at the London 2012 Olympics, has faced racial abuse on Twitter since that incident.
A Metropolitan Police spokesman said the arrests were made over alleged public order offences.
"Six males were arrested during the game at Millwall in relation to a banner being unfurled at the game," he said.
"They remain in custody at this time. The banner on display today was swiftly removed by Millwall staff."
The club 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 took to Twitter after the Millwall match last month to claim himself and team-mates Lee Chung-young, Darren Pratley and Benik Afobe were subjected to racist taunts.
That sparked an investigation led by both clubs and last week Millwall confirmed the boy in question admitted to abusing Sordell and subsequently issued a written apology which the player accepted.
Given his age, Millwall have not imposed a life ban on the youngster and offered him a place on a "Millwall for All" educational programme, "in the hope that we can change his outlook on equality, racism and life in general".