Roth told The Associated Press that the board of the nonprofit group is meeting in Brazil for the first time in its 41-year history due to its concerns about the South American country's far-right administration.
"Today is by far the most worrying visit I've had to present, and what's concerning is that we have a president now who is openly speaking with anti-rights rhetoric," said Roth, who has headed Human Rights Watch since 1993 and is making his fourth visit to Brazil.
He accused Bolsonaro of giving a green light to illegal police killings, undermining anti-torture initiatives and blocking the prosecution of groups that caused fires in the Amazon this year.
The administration of Bolsonaro, who began a four-year term Jan. 1, did not respond to requests for comment on Roth's statements.
Roth said the president is getting intense pushback from other democratic institutions, "but will remain in a very powerful position" for the next few years.
"The Brazilian Congress has stopped some of (Bolsonaro's) worst efforts to undermine the laws restricting police violence. We've seen the courts step in and block efforts to undermine the anti-torture body or to regulate Brazilian NGOs. We have seen activists and journalists speaking out about these problems. There is a political battle underway for this political soul of Brazil," Roth said.
He also criticized Bolsonaro's silence about Venezuela's candidacy for a seat on the United Nations' human rights council. In Thursday's vote in New York, Brazil, Venezuela and last-minute bidder Costa Rica are vying for two Latin America's two spots at the body. Brazil is seeking re-election to its seat.
"The Brazilian government is, in essence, accepting a Venezuelan candidacy. Brazil has not urged governments around the world to vote against Venezuela, and for Costa Rica," Roth said. "That's what it should do if it's going live up to what it claims is its opposition to the Venezuelan dictatorship."
Roth said that despite his worries about Brazil, he is far more concerned about neighboring Venezuela.
"We hope Brazil never gets that far down the road," he said.