Officials said they found bricks and rocks hidden in strategic places on street corners in Brooklyn and Queens.
The boxes were not in the vicinity of any protests, but the NYPD believes they were to be picked up to be used at a future protest.
Police Commissioner Dermot Shea said bricks were recently stolen from a construction site in Manhattan, and police are looking into if that burglary is connected.
He also revealed that "seemingly innocuous plastic bottles" thrown at police during protests "are often filled with cement."
Along with being thrown at officers, protesters are also throwing the bottles at police cruisers, causing large amounts of damage.
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