Millwall say they are "dismayed and saddened" after some of their fans booed players taking a knee at the start of Saturday's game against Derby.
The Den was able to host 2,000 home fans for the first time this season after the second national lockdown was lifted.
However, the return of spectators was overshadowed by the pre-match incident.
The Football Association and anti-discrimination body Kick It Out have also condemned the booing.
"Millwall Football Club was dismayed and saddened by events which marred Saturday's game against Derby County at the Den," said the club in a statement.
"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."
'An absolute disgrace'
Derby boss Wayne Rooney, whose side won Saturday's game 1-0, said it was "disappointing and upsetting" to hear the booing from supporters.
"I'm pleased with how my team dealt with that," he added. "They've had to put that to the back of their minds for the 90 minutes but I'm sure it's something they were thinking about."
Derby forward Colin Kazim-Richards described the incident as "an absolute disgrace".
Some boos were also heard when players took the knee at League Two Colchester United's JobServe Community Stadium, before the home side's 2-1 win over Grimsby Town in front of around 1,000 spectators.
Forward Callum Harriott, who scored the winner, later called the booing "ridiculous" and said it left him "absolutely disappointed".
His club said it was "fully behind any and all of our players and staff who take a stand against any form of discrimination", adding: "We also condemn the behaviours of any supporters that actively voice opposition to those activities."
Players, officials and staff at Premier League and English Football League games have been taking a knee pre-match since football restarted in June in order to show their support for the Black Lives Matter movement for racial equality.
'We have come so far but we have so far to go' - reaction
Former Manchester City and England defender Micah Richards described the Millwall incident as "disheartening".
"How do these fans get allocated to the games?" he said on BBC Final Score.
"There are 2,000 so you can pinpoint the people going. There are no excuses. I am sick to death of talking about this situation.
"It is so disheartening because it is like we have come so far but we have so far to go. I don't even like talking about the matter. It feels like it falls on deaf ears. It is time and time and time again."
Former Coventry and Aston Villa striker Dion Dublin, who had a loan spell at Millwall in 2002, added: "They don't agree with taking the knee, which means they are racist. They don't agree with Black Lives Matter; that says they are racist to me.
"It says to me that a minority of Millwall fans are spoiling it for a club that is going in the right direction with a tag they have had for years and years and they are trying to eradicate it."
On Friday, Millwall's first-team squad issued a statement supporting efforts to rid the game "of all forms of discrimination".
After Saturday's match, Lions boss Gary Rowett told Sky Sports: "I'm disappointed that we are talking about that when we should be talking about the fact we are all back and we want to enjoy the football match again.
"The club does an enormous amount of work on anti-racism and the club do a lot of work in the community and there is some really positive stuff, so of course I am disappointed."
'We applaud the players for defying the hate'
A Football Association spokesperson said: "The FA supports all players and staff that wish to take a stand against discrimination in a respectful manner, which includes taking of the knee, and strongly condemns the behaviours of any spectators that actively voice their opposition to such activities."
Kick It Out chair Sanjay Bhandari said he was "saddened" by the booing and praised the teams for "defying the hate" shown by some members of the crowd.
"What this demonstrates is that players are right to continue standing up to discrimination, whether that is through taking the knee or speaking out," he added.
"The fight for racial equality continues and we will continue to work closely with clubs across the country to tackle discrimination in all its forms.
"We applaud the players for taking a stand and defying the hate shown today."
The English Football League said: "The EFL continues to support any individual player, players and clubs who choose to 'take the knee' in support of tackling inequality in society.
"We are disappointed that a small group of supporters have today chosen to voice their opposition to such activities directly aimed at raising awareness of the fight against racism."
American football player Colin Kaepernick started kneeling symbolically during the pre-game national anthem in the NFL in 2016, in protest at police violence against African-Americans in the United States.
The Black Lives Matter movement and taking a knee has grown in prominence in the UK following the death of George Floyd in the US in May, which sparked protests around the world.
The 46-year-old, an unarmed black man, died after a white police officer held a knee on his neck for nearly nine minutes.
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