It has been replaced by effigies of former President George W. Bush and Hillary Clinton.
Manager Tom Whalen says it's to show the "Walkin Charlie" game isn't "anti-Democrat or "anti-Republican."
The game requires patrons to throw baseballs at plates held by the rotating caricatures.
A plastic bag was placed over the Obama character's head after some people earlier this week said it was disrespectful to use the president's likeness.
Whalen says a Secret Service agent visited the Seaside Heights concession on Wednesday and told him none of his employees had urged patrons to throw at or hurt Obama.
Whalen says the Obama figure might return in a few weeks.
Information from: The Star-Ledger, http://www.nj.com/starledger