Officers "should have done a better job," Scott told the San Fransisco Chronicle in an interview.
"I'm sorry that this happened. I'm sorry to the people of San Francisco. I'm sorry to the mayor. We have to fix it. We know there were some concerns in that investigation and we know we have to fix it," he added.
The police chief told the newspaper that he was "concerned" that warrants for the raid on freelance videographer Bryan Carmody's home and office did not sufficiently recognize him as a journalist.
Scott told the newspaper that an independent agency would conduct an internal affairs investigation, which could lead to officer discipline. He noted that police will not use evidence from the raid.
Police searched Carmody's home while investigating the leak of a report that contained unflattering information about Public Defender Jeff Adachi before his death.
Scott's apology is a reversal of his previous defense of the raid. He said Tuesday that police suspected Carmody conspired to steal a police report, which Carmody denied.
A week before that Scott said, "We went through the legal process and the appropriate legal process for a criminal investigation."
Scott's apology also follows much public pressure and condemnations from high-profile California politicians including Gov. Gavin Newsom (D) and Sen. Kamala Harris (D).