Alongside his brother Wesley, Batista owns the world's biggest meatpacking company, JBS, and previously struck a plea bargain with graft investigators in return for testifying to the bribing of politicians.
The brothers have admitted to bribing 1,900 politicians and have even testified against President Michel Temer.
Police said in a statement that the arrests were part of an operation aimed at "dismantling a criminal organization operating in the Chamber of Deputies and the Ministry of Agriculture."
The two former agriculture minsters arrested were Antonio Andrade, currently the vice-governor of Minas Gerais state, and Neri Geller.
At the time they held their agriculture ministry roles, in 2013-14, they were members of Temer's MDB party.
In total 19 people were arrested, among them a current deputy, JBS executives, lawyers and former agriculture ministry officials, while 64 raids were carried out in five states.
Investigators claim that JBS bribed agriculture ministry officials through political intermediaries in order to obtain benefits from industry regulations and the attribution of commercial licenses.
These bribes gave JBS advantages over its competition and the possibility to "build a market monopoly," police said.
JBS allegedly paid two million reis ($590,000 at the 2015 exchange rate) to manipulate regulations in ways that would give it an advantage over competitors.
Joesley Batista was previously held between September 2017 and March of this year on suspicion of having withheld information from prosecutors, something that saw him stripped of his plea bargain.
The information he and his brother gave led prosecutors to request two investigations into allegations that Temer paid bribes to buy the silence of a deputy, but on both occasions the Chamber of Deputies blocked the investigations' progress.
The Car Wash investigation has ensnared some of Brazil's biggest companies, such as construction conglomerate Odebrecht and state oil giant Petrobras, and some its most notable politicians, including former president Luiz Inacio Lula da Silva, who is currently serving a 12-year prison sentence for accepting a bribe.
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