One of the orders issued late Tuesday, hours after his inauguration, likely will make it all but impossible for new lands to be identified and demarcated for indigenous communities. Areas set aside for "Quilombolas," as descendants of former slaves are known, are also affected by the decision.
Another order removed the concerns of the LGBT community from consideration by the new human rights ministry.
In a move favorable to his allies in agribusiness, which have criticized giving large swaths of lands to the indigenous, Bolsonaro transferred the responsibilities for delineating indigenous territories from the Justice Ministry to the Agriculture Ministry. The new agriculture minister, Tereza Cristina, is part of the agribusiness caucus in Brazil's lower house and has opposed requests from native communities.
Bolsonaro, a former army captain and longtime congressman, said during his presidential campaign that he would stop making what he calls concessions to native Brazilians and quilombolas.
"Less than one million people live in those places isolated from the real Brazil," Bolsonaro tweeted Wednesday. "They are explored and manipulated by nonprofits. Together we will integrate those citizens and give value to all Brazilians."
The Justice Ministry previously handled demarcation of indigenous lands through the FUNAI agency, which also oversees other initiatives for indigenous communities such as health care, housing and language preservation. Bolsonaro's order is raising uncertainties about FUNAI by shifting it to a new ministry for family, women and human rights that is headed by an ultraconservative evangelical pastor.
Indigenous leader Sonia Guajajara said the presidential order aims to dismantle protections for Brazil's indigenous communities.
"Does anyone still doubt his promises to exclude us during the campaign?" she asked on Twitter.
Bolsonaro said last year that he also wants to annul land demarcation decisions made by previous administrations, but legal experts say recent Brazilian Supreme Court rulings could block such move.
New Health Minister Luiz Henrique Mandetta, meanwhile, suggested on Wednesday that there will be spending cuts in health care for the indigenous.
"We have figures for the general public that are much below what is spent on health care for the indigenous," he said, without providing details.
In removing LGBT concerns from the responsibilities of the human rights ministry, Bolsonaro did not name any agency to consider such things. He has strongly criticized what he calls "gender-based ideology," saying it is a threat to Brazil's Christian values.
LGBT activist Symmy Larrat said she doesn't' expect reasonable treatment from the Bolsonaro administration.
"The human rights ministry discussed our concerns at a body called secretariat of promotion and defense of human rights. That body just disappeared, just like that. We don't see any signs there will be any other government infrastructure to handle LGBT issues," she said.
The newspaper Folha de S.Paulo reported that Bolsonaro will later announce the closing of an agency within the Education Ministry that has been aimed at promoting diversity in public schools and universities.
Bolsonaro, a fan of U.S. President Donald Trump, met with Secretary of State Mike Pompeo on Wednesday.
Pompeo told him that Trump is "very pleased with the relationship that our two countries are on the precipice of beginning to develop."
"He's also confident that it (the relationship between the U.S. and Brazil) will benefit the world and the set of shared values that we believe we can together advance," Pompeo said before leaving Brasilia for Colombia.
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