Indigenous leaders and specialists working with Brazil’s nearly one million tribal people have been stunned and disconcerted by the appointment of a federal police officer with strong connections to agribusiness as the new head of the country’s indigenous agency.

Marcelo Xavier da Silva’s confirmation as the new president of the Funai agency is in line with far-right president Jair Bolsonaro’s plans to develop indigenous areas which include some of the most protected reserves in the Amazon. Critics said the move effectively puts Brazil’s powerful agribusiness sector in charge of indigenous affairs.

“We are worried that indigenous policies may not be properly carried out, considering the history of this president,” said Andrea Prado, president of a Funai staff association.

“He is not technically prepared … he is not an indigenous specialist,” said a former Funai employee who knows Xavier da Silva, adding: “I am scared of him.”

Xavier da Silva, 41, worked on a controversial Congress inquiry in 2017 that attacked Funai and government land agency Incra and recommended charges against some employees as well as anthropologists, campaigners, prosecutors, “supposed indigenous” people and a former justice minister .

The inquiry concluded that Funai had become a hostage to “external interests and ideological objectives” and contended that some Brazilian NGOs were funded by international groups connected to US farming interests.

During a series of land disputes in Mato Grosso do Sul state later in 2017, Xavier da Silva – then the Funai ombudsman – wrote to federal police asking them to take “persecutory measures” against indigenous groups in the region.

The new Funai president “has a long history campaigning and working against indigenous people – he was always in favour of farmers”, said Dinamam Tuxá, executive-coordinator of the Articulation of Indigenous Peoples of Brazil.

Xavier da Silva was also nominated as an aide to Nabhan Garcia, a senior agriculture ministry official and president of an agribusiness lobby, but federal police declined to cede him, BBC Brasil reported. In June, the outgoing Funai president, Gen Franklimberg de Freitas, said Garcia “froths hate” for indigenous people and sees Funai as “an obstacle to national development”.

Outgoing Funai president of Franklimberg de Freitas. Photograph: Ueslei Marcelino/Reuters

Bolsonaro has repeatedly criticised the agency, which he has described as “a nest of rats”. On Friday, the president attacked foreign media perceptions of Brazil’s indigenous people.

“You want the indigenous people to carry on like prehistoric men with no access to technology, science, information and the wonders of modernity,” he told reporters.

“Indigenous people want to work, they want to produce and they can’t. They live isolated in their areas like cavemen. What most of the foreign press do to Brazil and against these human beings is a crime.”

Xavier da Silva’s appointment won support from leading agribusiness figures when it was announced on Friday. Nilson Leitão, the former congressman who led the congress inquiry and also led the most powerful agribusiness lobby in Congress, praised the decision.

“He has expertise and vast knowledge,” he said. “I have no doubt he is fit to do a good job – provided they give him the necessary support.”