The new law would increase penalties for rioting or inciting rioting that causes damage to property, serious injury or death.
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Cooper vetoed a similar bill last year and showed in a statement his concerns remain.
"I acknowledge the changes that were made to modify this legislation's effect after my veto of a similar bill last year," Cooper said. "Property damage and violence are already illegal, and my continuing concerns about the erosion of the First Amendment and the disparate impacts on communities of color will prevent me from signing this legislation."
Marques Thompson of Democracy North Carolina feared the bill could potentially silence more voices.
"It potentially criminalize protests and make it so that people who are peacefully protesting now, because of how vague this law is written, now could be charged with a felony and lose their right to vote," Thompson said.
The bill was inspired by the demonstrations in downtown Raleigh following the death of George Floyd.
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"It was already illegal to damage property and yet this bill makes three or more people subject to being called a "riot" when people are protesting," Thompson said. "When people decide to protest, they do it peacefully. They're always trying to be. No one wants destruction of property."
While the previous version of the bill was met with strong opposition from Democrats, H.B. 40 cleared the Senate in March with a single Democrat joining Republicans.
"I am pleased that this bipartisan legislation will finally become law," North Carolina House Speaker Tim Moore said. "While the First Amendment guarantees the right to peacefully protest, those who hijack otherwise peaceful demonstrations to cause chaos and destruction in our communities must be held accountable, and law enforcement must have our support to do just that."