The Indigenous Affairs department (FUNAI) claims Steve Campbell risked exposing the Hi-Merimã tribe to disease and death last month.
In a statement seen by Thomson Reuters Foundation, a spokesman said: "It's a case of rights violation and exposure to risk of death to isolated indigenous population.
"Even if direct contact has not occurred, the probability of transmission of diseases to the isolated is high."
Mr Campbell, who belongs to Greene Baptist Church in the US state of Maine, told the Folha de São Paulo newspaper he was in the area by accident.
Unbelievably, just a few months after John Allen Chau tried to contact the #Sentinelese, ANOTHER missionary is reported to have tried to contact an #uncontacted tribe. When will they stop?https://t.co/ohd8ckvDPD
— Survival International (@Survival) January 22, 2019
Located in the north-western state of Amazonas, the Hi-Merimã is one of a number of tribes in Brazil which has virtually no contact with the outside world.
Virtually cut off from wider society, remote tribes may not benefit from vaccinations.
Stephen Corry, from Survival, a group which supports tribal peoples, said: "Fundamentalist Christian American missionaries must be stopped from this primitive urge to contact previously uncontacted tribes.
"It may lead to the martyrdom they seek, but it always ends up killing tribespeople."
Officials say they will notify federal prosecutors and the police. It remains unclear what action Mr Campbell could face.
He has been living among another tribe, the Jamamadi, for years - albeit without permission, according the Indigenous Affairs department.
Last November, Premier reported how an American Christian man (pictured) was killed by tribespeople on an isolated island in the Indian Ocean.
Stay up to date with the latest news stories from a Christian perspective. Sign up to our daily newsletter and receive more stories like this straight to your inbox every morning.