Ammon Bundy, who has led the revolt in rural Oregon, was one of seven people arrested after a stand-off pitting an anti-government militia against the US authorities.
Bundy has said protesters acted at the request of a rancher who wanted to graze his 600 cattle on federal property, but was prevented from doing so when the US Fish and Wildlife Service (USFWS) installed a fence last year.
Bundy, 40, was arrested along with six others who face "a federal felony charge of conspiracy to impede officers of the United States from discharging their official duties through the use of force, intimidation, or threats," the FBI said.
Authorities did not immediately identify the person who was killed.
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"One individual who was a subject of a federal probable cause arrest is deceased," and another person was injured and receiving medical treatment, the FBI statement added.
The activist group which took over the Malheur National Wildlife Refuge was protesting the jailing of two local ranchers, Dwight and Steven Hammond, who were convicted of arson.
They were calling for the government to turn over federal land in the area to the people.
Some neighbors and members of the local community, notably the Oregon Cattlemen's Association, rejected the takeover, even if they support the Hammonds' plight.