Metropolitan Police confirmed that a 53-year-old from Enfield was arrested for a racially aggravated public order offence and remains in police custody.
The development comes the day after Sky Sports News broadcast a Special Report on racism in football that appeared to show striker El Hadji Diouf being abused at The Den during a game in November.
Both the Metropolitan Police and the Football Association requested a copy of Monday's programme to conduct their own investigations.
Millwall released a statement after the broadcast to say they were "appalled" by the footage.
The Championship club has promised to ban any individuals for life if they are found guilty.