Starbucks “stands firmly against discrimination or racial profiling,” chief executive Kevin Johnson said in a statement.
He said he wants to meet with the men to offer a “face-to-face apology”.
A video posted online shows police handcuffing the men after a quiet discussion that lasted several minutes.
Police Commissioner Richard Ross said Starbucks employees called 911 to say the men were trespassing.
He said officers were told the men had come in and asked to use the toilet, but were denied because they had not bought anything. He said they then refused to leave.
Mr Johnson’s statement did not address exactly what led to the police call, but a Starbucks spokeswoman said the store where the arrests occurred has a policy that restrooms were for paying customers only.
In the video, no Starbucks items are visible in front of either of the men.
Mr Johnson said the company’s practices and training led to a “bad outcome”, and the reason for the call that brought police into the shop was incorrect.
“Our store manager never intended for these men to be arrested and this should never have escalated as it did,” said the statement.
Mr Johnson said videos of the arrest were “very hard to watch”, and the company was investigating.