It happened in the early morning hours Saturday.
Officials said during the encounter, shots were fired and the man shot died at the scene.
WATCH: Full news conference by the Nash County Sheriff's Office
Family identified the man shot as 28-year-old Jonathan Ramirez.
Sheriff Keith Stone said a woman reported a sexual assault and that the "female subject who called in the sexual assault had kind of coached law enforcement to where he was at."
That led them to Ramirez.
Sheriff holding press conference in Nash County NC regarding the deputy involved shooting death of Jonathan Ramirez. Family says it was not justified. We’ll learn more soon. Watch live on https://t.co/9OhQVn1uuM pic.twitter.com/ut85Gge7HI— Tim Pulliam (@TimABC11) February 11, 2019
The Nash County Sheriff's Office said body camera footage of the incident does exist and is being looked at.
Deputies say body cameras show Ramirez exiting his vehicle with a loaded gun before the shooting.
It's a claim Jonathan's father denies.
"He did not point a gun. That gun was empty," said Rick Ramirez. "You will find out when everything progresses. The gun was empty."
The Sheriff's Office said Monday that Ramirez's gun was loaded.
The family said Ramirez was headed to meet his fiancee that morning and said there were no officer commands or flashing lights to warn Ramirez.
The sheriff said Ramirez was well aware that deputies had pulled him over for a sexual assault allegation.
"There's no doubt in your mind he knew he was dealing with law enforcement before he was shot," Stone said. "If I can stress this ... put your hands 10 and 2 on the steering wheel - turn the dome light on in the vehicle and comply."
Ramirez's family says they believe deputies were searching for the wrong person and that Jonathan was not the person involved with the original call.
"My niece says 'your son has been killed,' said Francisca Ramirez, Jonathan's mother. "I thought they were here to defend him, to protect him from whoever shot him, and it was them that shot him. There is no way you can describe that."
It's not clear how many times Ramirez was shot.
Three deputies are on leave while an internal investigation takes place, along with the standard SBI investigation whenever a law officer is involved in a shooting.
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