The city said earlier that the person had died, then retracted the statement.
"Civilian who suffered gunshot wound during protests is on life support, critical condition. Not deceased," the city said on Twitter.
Authorities had said the protester was shot by a civilian, adding that police did not open fire.
An AFP reporter at the scene of the protests outside the Omni Charlotte hotel saw a man who was apparently shot falling to the ground, bleeding heavily.
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Some demonstrators banged on windows, others threw objects at police and stood on cars. Police fired what appeared to be tear gas, sending the protesters scattering.
"We are working to bring peace and calm to our city. We know this is not who Charlotte is," Mayor Jennifer Roberts said on CNN, calling on people to stay home and off the streets.
"Tell everyone that violence is not the answer," she said.
Roberts added that authorities would consider other options if violence continues to flare, "possibly curfews and that sort of thing, but right now, we are continuing to work with what we have tonight."
Sixteen officers and several demonstrators were injured in clashes overnight Tuesday following Scott's death, the latest in a string of police-involved killings of black men that have fueled outrage across the United States.
Earlier yesterday, presidential candidates Donald Trump and Hillary Clinton weighed in on the violence in Charlotte, which came on the heels of another fatal police shooting of a black man, Terence Crutcher, on Friday in Tulsa.
"Keith Lamont Scott. Terence Crutcher. Too many others. This has got to end. -H," tweeted Democrat Clinton, signing the post herself.
"I don't know what she was thinking," the Republican said, speaking at an African-American church in Cleveland, Ohio.