Police believe the former leader's vaccination record was faked in order for him to enter the US.
As part of the operation, police detained several of the former president's close associates and seized both their mobile phones as well as the phone used by his wife.
Bolsonaro has refuted all accusations of impropriety.
The former president has been outspoken in criticizing covid vaccines for spreading erroneous information about the shot and its purported negative effects.
Mr. Bolsonaro denied tampering with any data in a statement following the search. "For my part, there was nothing falsified," he told the press.
Additionally, he said, "I didn't take the vaccine. Period."
When Mr. Bolsonaro was still president in November and December of last year, it is claimed that false information was added to the records.
At the end of December, just days before his rival, Luiz Inacio Lula da Silva, took the oath of office, Mr. Bolsonaro travelled to Florida.
The US has not made any comments on the visa the former president used to enter the country or whether or not he presented any vaccination records at the time.
Mr. Bolsonaro has had to go before the police twice since his return to Brazil on March 30.