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Charges have been rescinded against a man accused of splattering red paint on an Israeli flag in Philadelphia because prosecutors say a second suspect was involved.

District Attorney Larry Krasner's office said in a statement on Friday that the charges against 26-year-old Antoine Guyton were rescinded because the investigation has shown a different man initially sprayed the flag with paint. However, they say Guyton also had a role in the vandalism.

An affidavit is being prepared for Guyton's re-arrest and police are seeking information on the other suspect.

Police responded to a report of a man spray painting the flag around 4pm on Tuesday. The suspect had fled, but Guyton appeared at the scene while officers were there and was taken into custody.

The incident happened a day after Israeli soldiers killed dozens of Palestinians protesting on the Gaza border.

At the time of the incident, Mayor Jim Kenney confirmed the initial suspect was taken into custody and decried the vandalism as hateful.

Kenney said "emotions are running high" after Israeli soldiers killed dozens of Palestinian civilians protesting on the Gaza border on Monday. 

The protests in Gaza were driven by anger over the controversial relocation of the US embassy in Israel from Tel Aviv to Jerusalem, as well as calling for their right to return on the day of the Nakba.

"While I understand that emotions are running high and there are many viewpoints stemming from recent violence against Palestinians and other protesters in the Gaza Strip, it doesn't warrant hateful acts of vandalism," he said.

Out of Gaza's 1.9 million population, 1.3 million of them are refugees or relatives of Palestinians from the pre-1948 borders who fled their homelands during the Nakba, or the Catastrophe.

Nakba saw the expulsion of more than 700,000 Palestinians to create Israel.  

The suspect's name has not been released. The flag hangs along a major boulevard as part of a display of world flags.