The appointment comes as Jair Bolsonaro won a sweeping election victory last week, with pledges to combat corruption.
He made it clear after his win that he wanted judge Sergio Moro to join his administration, saying he was a person of “extreme importance in a government like ours”.
Moro said last week it was an honour to be asked to oversee justice and public security.
The judge has uncovered a number of corruption cases involving top-level politicians from a broad spectrum of parties.
Moro’s supporters see him as an anti-corruption leader but others have accused him of targeting left-wing politicians, especially those in the former ruling Worker’s party.
Former president Luiz Inacio Lula da Silva, who is convicted as part of an anti-corruption investigation known as Operation Car Wash, has repeatedly said he is a victim of a political witch-hunt.
Moro was the judge in charge of the so-called ‘operation car wash’ investigation, which looked into claims that executives at the state oil company Petrobras accepted bribes in return for awarding contracts to construction firms.