Bolsonaro’s health records say he received the vaccine in Sao Paulo in 2021.
But an investigation later found he was not in the city at the time.
Bolsonaro, a Covid sceptic who publicly vowed never to have the vaccine, has denied any knowledge of records being tampered with.
Almost seven hundred thousand people have died of Covid-19 in Brazil, according to Johns Hopkins University in the US.
The federal police accuse Bolsonaro, who regularly downplayed the severity of the virus, and eight other people of plotting to issue “false certificates to obtain undue advantages” during the pandemic.
Vaccination was an entry requirement for many countries, including the US.
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