Brazil's Federal Police said it had detained "people who would be obstructing" the probe.
"Braga Netto was arrested in the operation," the source said.
In late November, police released a report recommending the indictment of far-right Bolsonaro and several dozen allies for attempting a coup d'etat to prevent the inauguration of leftist Luiz Inacio Lula da Silva.
The list included Braga Netto, who was also Bolsonaro's running mate in the 2022 elections.
Attorney General Paulo Gonet has been examining the allegations to see if evidence supports charges being laid against Bolsonaro and the 36 others named as co-conspirators.
Police served search warrants on the general as well as an advisor, Colonel Flavio Botelho Peregrino.
The 884-page report drawn up after a nearly two-year police investigation urges Gonet to indict Bolsonaro and the others for planning an attempted coup and seeking to "violently overthrow the democratic state."
It details alleged collusion between Bolsonaro, 69, and some of his officials, including members of his military brass, to claim fraud in the 2022 elections won by Lula and to use decrees to sideline the Supreme Court.
"The then-President of the Republic, Jair Bolsonaro, actively participated in the creation of the coup plan, being directly involved in the drafting of documents and strategies to remain in power, even after the electoral defeat," the report said.
Bolsonaro was also "fully aware" of an alleged plan by elite soldiers to assassinate Lula, his vice president and a Supreme Court judge, said the report.
It said Braga Netto had an "active participation" in the effort to pressure commanders of Brazil's armed forces to "join the coup project."
The plan, called "Green and Yellow Dagger," was allegedly discussed at Braga Netto's home.
It was printed at the Planalto palace, the seat of the Brazilian presidency, according to investigators.
A draft of the coup plot was found at the headquarters of Bolsonaro's Liberal Party among the belongings of one of Braga Netto's advisors.
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