RIO DE JANEIRO — President Jair Bolsonaro of Brazil, who has compared indigenous communities living in protected lands to animals in zoos, took a major step toward undermining the rights of indigenous people just hours after taking office on Tuesday.

In one of a handful of measures that stand to hurt historically marginalized communities, the incoming government on Tuesday transferred responsibility for certifying indigenous territories as protected lands to the ministry of agriculture. The ministry has traditionally championed the interests of industries that want greater access to protected lands.

The certification was previously overseen by the National Indian Foundation, a government agency tasked with safeguarding the rights and welfare of indigenous communities.

Mr. Bolsonaro, a far-right former lawmaker and Army captain, presented himself to voters as the polar opposite of the leftist Workers’ Party, which championed the advancement of poor and disenfranchised communities. The party lost the presidency during impeachment proceedings in 2016 as Brazil was beset by a recession, rising violence and a corruption scandal.