Several other locations were also searched and six people faced arrest.
The former president confirmed the search on his residence in the capital Brasilia as he stood outside the building.
A federal police official said Mr Bolsonaro would be questioned at Federal Police headquarters and confirmed that one of his closest allies, Mauro Cid, had been arrested.
The Federal Police’s press office said officers had been carrying out 16 searches and six arrests in Rio de Janeiro related to the introduction of fraudulent data related to the Covid-19 vaccine into the nation’s health system. The statement did not name Mr Bolsonaro or Mr Cid.
Local media reported that the vaccine cards of Mr Bolsonaro, his advisers and his family members were altered.
During the pandemic, he spent months sowing doubts about the efficacy of the vaccine and refusing to get a jab.
In September 2021, that prompted doubt about whether he would be able to attend the UN in New York.
“There was no adulteration on my part, it didn’t happen,” he insisted yesterday. “I didn’t take the vaccine, period. I never denied that.”
The search adds to Mr Bolsonaro’s mounting legal headaches. Federal Police have questioned him at their Brasilia headquarters twice in the past month regardin g separate investigations, into he received three sets of diamond jewelery from Saudi Arabia, and his potential role in sparking the January 8 uprising by his supporters in the capital.
Mr Bolsonaro is also the subject of several investigations by Brazil’s electoral court into his actions during the presidential election campaign, particularly his unsubstantiated claims that the nation’s electronic voting system is susceptible to fraud.
Those threaten to strip him of his political rights and render him unable to run for office in upcoming elections.
Separately, Mr Bolsonaro and his allies face a sprawling Supreme Court-led investigation regarding the spread of alleged falsehoods and disinformation in Brazil.
There is also a federal police investigation into the alleged genocide of the i indigenous Yanomami people in the Amazon rainforest by encouraging illegal miners to invade their territory and thereby endangering their lives.
The former president has denied wrongdoing in all of the cases that are under investigation.
The police statement said the insertion of false Covid-19 data occurred between November 2021 and December 2022, and enabled the people whose vaccine cards were altered to comply with the US vaccine requirements to enter the country.