"I didn't want any television show about my family to include a guy who owned slaves ... the very thought left a bad taste in my mouth."
The 42-year-old is known for supporting an array of humanitarian causes and founded the Eastern Congo Initiative in 2010.
Affleck said the process of delving into your family past makes you quite vulnerable, and he didn't want to bring public shame to his relatives.
Nevertheless, the Gone Girl actor said he regrets his decision.
"We deserve neither credit nor blame for our ancestors and the degree of interest in this story suggests that we are, as a nation, still grappling with the terrible legacy of slavery," Affleck wrote.
"I am glad that my story, however indirectly, will contribute to that discussion," he said.
The star of the upcoming blockbuster Batman v Superman: Dawn of Justice also stressed that the show, which aired in October, wasn't a news program.
US TV network PBS has since launched an internal review over the matter.
PBS and Harvard scholar Henry Louis Gates, host of the show, said they didn't censor the slave-owner details.
Instead, more interesting ancestors of the actor emerged, and Gates chose to highlight them instead.
The show traces the ancestry of well-known guests.
- AAP
