Making a surprise appearance at the daily White House press briefing, Mr Obama said he should have chosen his words more carefully at his Wednesday news conference.
"Because this has been ratcheting up and I obviously helped to contribute ratcheting it up, I wanted to make clear in my choice of words I think I unfortunately gave an impression that I was maligning the Cambridge Police Department or Sgt Crowley specifically," Mr Obama said.
"I could have calibrated those words differently," he added.
Mr Obama also revealed that he had spoken to Sgt Crowley on the telephone, and described him as an "outstanding police officer and a good man".
He said he continued to believe that Professor Gates's arrest was "an overreaction", but that "Professor Gates probably overreacted as well".
On Wednesday, Mr Obama had said: "The Cambridge police acted stupidly in arresting somebody when there was already proof that they were in their own home."
Professor Gates leads the African American research centre at Harvard
And he put the arrest in the context of "the long history in this country of African-Americans and Latinos being stopped by law enforcement disproportionately".
Critics seized on his comments, saying the president should not be getting involved in individual cases, especially if he was not in full possession of the facts.
Officers were called to Prof Gates's house after a woman reported seeing two black males - the professor and his driver - trying to force entry.
Prof Gates's lawyer later said the professor had just returned from a trip overseas and, upon arriving at the property with a driver, found his front door jammed and had to force it open.
Although the exact facts of the incident are disputed, Prof Gates was asked to provide the officer with identification. He was then asked to step outside his house and was arrested.
According to police, Prof Gates shouted at the officer and accused him of racial bias.
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