Authorities said the incident happened Sunday around 2 a.m.
Time stamps on surveillance video shows what appears to be three young men taking the flags from atop of the building on West Edenton Street.
"We don't have anything that indicates it was meant to be malicious but even it wasn't we take it as that. Like I said it's theft of state property, it's theft from everyone," said State Capitol Police Sgt. Thomas Fowler.
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The individuals can be seen entering the frame empty handed and walking back into the picture moments later with the flags in their possession.
Officials believe the suspects accessed the flag poles on the roof of the building via construction scaffolding.
"We hope to identify these suspects with the help of the public," said State Capitol Police Chief Glen Allen in a news release. "These flags were stolen from the people of North Carolina, and larceny should not be tolerated."
Anyone with information on the three suspects may call the State Capitol Police at (919) 733-3333.