The Championship club insisted they were “dismayed and saddened” by the events which marred their 1-0 defeat at home to Derby on Saturday.
It is understood those responsible are unlikely to face punishment because they have not broken any club rules.
But Millwall will take the knee in support of the Black Lives Matter movement again for the visit of Rangers - who ditched the gesture earlier this season.
QPR director of football Les Ferdinand said in September that the impact of kneeling has been “diluted” and claimed it had “reached the point of good PR but little more.”
Millwall will meet with anti-discrimination group Kick It Out after condemning Saturday’s unsavory scenes, to search for short and long term solutions to the issue.
The south London club said in a statement: “Millwall Football Club was dismayed and saddened by events which marred Saturday’s game against Derby County at The Den.
“The club has worked tirelessly in recent months to prepare for the return of supporters and what should have been a positive and exciting occasion was completely overshadowed, much to the immense disappointment and upset of those who have contributed to those efforts.
“The impact of such incidents is felt not just by the players and management, but by those who work throughout the club and in its Academy and Community Trust, where so many staff and volunteers continue passionate endeavours to enhance Millwall’s reputation day after day, year after year.
“The club will not allow their fine work to be in vain. The players are continuing to use the biggest platform they have to support the drive for change, not just in football but in society generally.
“There is much work to be done and at Millwall everyone is committed to doing all that is possible, both individually and collectively, to be a force for good and to ensure that the club remains at the forefront of football’s anti-discrimination efforts.”
Environment Secretary George Eustice landed himself in hot water yesterday for defending the Millwall fans who booed.
The Conservative MP for Camborne and Redruth said: "If people choose to express their view in a particular way, that should always be respected.
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“My personal view is that Black Lives Matter is actually a political movement that is different to what most of us believe in, which is standing up for racial equality.
“But each individual can take their own choice about how they reflect this, and I know a number of people feel quite strongly and have taken that approach.”