Gannett Co has now asked the FBI to investigate, after it estimated that half of the newspaper's Facebook following was automated.
Facebook has removed millions of the fake accounts, but it has detected more suspicious activity since.
And the number of "likes" on the page has fallen from 15.2 million to 8.2 million due to the account deletions,
"We don't know why the scope of impact on USA Today's Facebook page appears greater than any other publisher," said Facebook spokeswoman Shabnam Shaik, in a report by USA Today on the issue.
The bots were observed commenting on stories, replying to each other and "liking" posts - as well as "liking" the USA Today page itself.
"From our point of view, we have done as much as we can in our control to solve the problem at hand," said Maribel Perez Wadsworth, an executive at Gannett Co.
"We look forward to Facebook resolving this issue on their platform so that we can move forward and positively engage our Facebook audience."
Proofpoint, a cyber-security firm used by Gannett Co, told the BBC it is continuing to investigate and track suspicious accounts on the page.
The BBC asked the FBI to confirm whether it had launched an investigation, but the bureau declined to comment.
Facebook did not respond to a request for comment.