The 1960s group advocated violence as a means to correct racial issues.
Former New York City mayor Rudy Giuliani said Beyonce's performance was an "attack" on police officers.
"This is football, not Hollywood, and I thought it was really outrageous that she used it as a platform to attack police officers who are the people who protect her and protect us, and keep us alive," he told FOX & Friends.
He continued, "And what we should be doing, in the African-American community and in all communities, is build up respect for police officers and focus on the fact that when something does go wrong, OK, we'll work on that."
During Queen B's performance, she donned a military-inspired outfit, with a gold "X" across her chest. Her backup dancers, meanwhile, donned berets, similar to berets worn by the Black Panthers.
They also raised their fists, as the controversial group did during its demonstrations.
To begin the performance, Bey and her crew formed an "X" in the field, which many media outlets are saying is a direct homage to Malcom X, a civil rights militant.
This could have all been written off a coincidence, but then photos emerged of one of Beyonce's dancers posing on the field with a sign reading, "Justice 4 Mario Woods," the black man shot and killed by San Francisco police officers.
Beyonce's mother, Tina, also posed with the black-clad dancers in which they held their fists in the air, again, like the Black Panthers.
"You might be the next Black Bill Gates in the Makin," she captioned the photo.
"I think it was outrageous. The halftime show I thought was ridiculous anyway," Rudy said in the aforementioned interview. "I don't know what the heck it was. A bunch of people bouncing around and all strange things. It was terrible."
Just before the performance, Beyonce released a new political song and video called "Formation." The harsh tone of the video and song was criticized by many in the mainstream media.
The music video is set in New Orleans and features a wall that reads "stop shooting us." She also appears on top of a police cruiser sinking in water. In another scene, a black child dances in front of a officers in riot gear.
She performed the new song at the Super Bowl. Many people began tweeting #BoycottBeyonce because of the song and because many felt disrespected by the political message.