Speaking to "TMZ Live," Anthony Galofaro, the owner of Milano Market, expressed his regret over Friday's incident and offered to "make a donation to a charity of Mr. Whitaker's choice to rectify this wrongdoing."
He said the employee who stopped the actor outside the deli was a "decent man" who was "just doing his job."
"We have a lot of shoplifters here," Galofaro said Monday. "It was very busy. He thought (Whitaker) took something and he wasn't sure."
The worker later apologized, but Galofaro said the man, a longtime employee, is "no longer here with us. … He doesn't want to come here, that's how much hurt he is. …It was a sincere mistake."
Still, Galofaro said he was unsure whether he would take the man back. "My job is to make sure this won't happen again," he said, adding that he is taking steps to retrain workers.
He also insisted that the incident had nothing to do with race. "It hurts me more than anything else what I've been hearing in the papers," he said about the accusations of racism.
Whitaker's rep, Jennifer Plante, did not respond immediately to ABCNews.com's request for comment, but she spoke out about the incident over the weekend.
"This was an upsetting incident given the fact that Forest did nothing more than walk into the deli," Plante told the New York Daily News. "What is most unfortunate about this situation is the inappropriate way store employees are treating patrons of their establishment."
According to Plante, the 51-year-old actor who won an Academy Award for his portrayal of dictator Idi Amin, opted not to call the cops over the incident, in part, because the worker was afraid of getting fired.
"Forest asked that, in the future, the store change their behavior and treat the public in a fair and just manner," she said.
Whitaker produced the Sundance standout "Fruitvale," based on the true story of a 22-year-old unarmed black man who was killed by a Bay Area transit policeman.