Den Bosch have apologised to Excelsior Rotterdam's Ahmad Mendes Moreira for declaring the striker mistook "crow sounds" for racist abuse during Sunday's Dutch second division match.
The referee brought the players off after half an hour as a result of the abuse from a section of the home fans.
"Den Bosch were completely wrong yesterday with its initial reaction," the club said in a statement.
"It appears there was racist abuse from the stands."
On Sunday the club stated that opposition players near the De Viert stand inside their De Vliert stadium were regularly treated to a "crow concert" by the home support.
But on Monday, they said: "That reaction was a blunder for which the club apologises to everyone, in particular to Excelsior player Ahmad Mendes Moreira.
"The club is further investigating what actually happened and will make every effort to find and punish those who are guilty of this."
Dutch football authorities have also opened an investigation into the incident.
Winger Moreira, 24, who was born in the Netherlands, said he was called a "negro and cotton-picker".
"I'm just very angry and very sad that these things still happen," he added.
Prosecutors will study camera footage and work with police to establish what happened during the match in the North Brabant region.
The game, which ended 3-3 with Moreira scoring in the 44th minute, restarted after a 10-minute delay.
It is the latest incident of racism in European football in recent months, which includes the abuse of England players in a Euro 2020 qualifier in Bulgaria, while Brescia striker Mario Balotelli threatened to walk off after being targeted by monkey chants during his side's away loss to Hellas Verona in Serie A.