Carlson was placed on the FBI's top ten most wanted list in September for his "alleged involvement in multiple armed sexual assaults in Los Angeles, California."
Believed to be 47-years-old, Carlson was thought to have been fatally shot at a hotel in Apex, a town roughly 15 miles west of Raleigh, FBI spokesperson Laura Eimiller told Fox News.
The bureau followed a lead from the Apex Police Department and "responded to a hotel room where we believed Carlson was staying. After an altercation, the suspect was shot and killed," the spokesperson said.
An investigation is now underway following the agent-involved shooting, officials said.
The fugitive who was listed as "armed and dangerous and an escape risk" was charged with one count of assault to commit rape in California in September 2017, and had allegedly been on the run since then, after he posted bond and fled to South Carolina, the FBI said. At some point, the FBI believes he obtained a stolen handgun, a rental car, and cash.
In November 2017, he led authorities on an "erratic, high-speed pursuit" in Alabama, before being spotted days later in Florida.
The following month, a federal arrest warrant was issued for Carlson and he was charged with unlawful flight to avoid prosecution.
The FBI said Carlson will be positively identified pending a review from the medical examiner's office.