Rights groups have called states out for everything from violence, threats to press freedom, arrests and smartphone surveillance implemented to fight the wave of infections.
"Against the background of rising ethno-nationalism, populism, authoritarianism and a pushback against human rights in some countries, the crisis can provide a pretext to adopt repressive measures for purposes unrelated to the pandemic," Guterres said in a statement.
"This is unacceptable."
He called on governments to be transparent, responsive and accountable.
"Civic space and press freedom are critical. Civil society organizations and the private sector have essential roles to play. And in all we do, let's never forget: The threat is the virus, not people," Guterres said.
The UN report on human rights and COVID-19 suggested that governments think about the consequences of their actions, saying "for better or for worse it is critical to consider the long-term whilst planning our short-term responses."