The Russia-related story, published on Thursday, reported Congress was investigating the ties of a Russian investment fund to an aide of U.S. President Donald Trump.
CNN had reported an internal investigation by its management found that certain editorial processes were not followed when the article was published.
The report said CNN had deleted the story from its website on Friday night after its investigation.
The story was replaced with an editor’s note of apology to Anthony Scaramucci, the Trump aide who was reported to be investigated in the story.
Trump has been critical of CNN, calling the news outlet “fake news” and refusing to take a CNN reporter’s questions at his first formal news conference earlier in the year after his Nov. 8 electoral win.