Supreme Court Justice Alexandre de Moraes on Friday night said the company had failed to fully comply with a previous ruling ordering the accounts to be shut down, saying they were still online and publishing by changing their registration to locations outside Brazil, according to Al-Jazeera.
Facebook issued a statement saying it had complied due to the threat of criminal liability for an employee in Brazil.
But it called the new order "extreme", saying it poses a "threat to freedom of expression outside of Brazil's jurisdiction and conflicting with laws and jurisdictions worldwide", and that it would appeal to the full court.
Facebook also argued it had complied with the previous order by "restricting the ability for the target Pages and Profiles to be seen from IP locations in Brazil".
"People from IP locations in Brazil were not capable of seeing these Pages and Profiles even if the targets had changed their IP location," the company said.
Moraes said Facebook should pay $367,000 in penalties for not complying with his previous decision during the last eight days.
He had also asked Twitter to block the accounts. While Twitter said then that the decision was "disproportionate" under Brazil's freedom of speech rules and that it would appeal, the targeted profiles were disabled.
Shortly after the judge's ruling on Friday, supporters of the president continued to publish anti-democratic slogans and personal attacks from changed location settings, the Folha de S Paulo newspaper reported.
Moraes is overseeing a controversial investigation to determine whether some of Bolsonaro's most ardent allies - such as right-wing activist Sara Winter from the "300 do Brasil" group - are running a social media network aimed at spreading threats and fake news against Supreme Court justices.
The probe is one of the main points of confrontation between Bolsonaro and the Supreme Court. The president himself filed a lawsuit last week demanding that the accounts be unblocked.