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A man accused of splattering red paint on an Israeli flag in the US state of Philadelphia has been taken into custody, local media reported.

Laura Frank, an employee of the Jewish Federation of Greater Philadelphia,  the Philadelphia Inquirer she saw a man standing near the flag with a paint gun on Tuesday and called police.

Democratic Mayor Jim Kenney confirmed a 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 al-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.