Facebook on Wednesday suspended a network of social media accounts it said were used to spread divisive political messages online by aides of Bolsonaro and two of his sons.
Nathaniel Gleicher, Facebook's head of cybersecurity policy, said the accounts were removed for using fake personas and other types of "coordinated inauthentic behaviour" which violated the company's rules.
He said there was no evidence the politicians themselves had operated the accounts.
Bolsonaro said "what is happening is regrettable" and a risk to "freedom of the press."
Facebook's allegations add to a burgeoning political crisis in Brazil, where Bolsonaro's sons and supporters have been accused of running a coordinated online campaign to smear the president's opponents.
The accusations have led to a congressional inquiry and a Supreme Court investigation into so-called "fake news attacks" on the country's judiciary, which led to police raids in May on the homes and offices of Bolsonaro allies.
Bolsonaro appeared alone on his weekly live broadcast on Facebook since he has tested positive for COVID-19. He coughed several times but looked healthy.
His press office said earlier on Thursday that the president "is getting on well, without complications."
