RIO DE JANEIRO — Federal prosecutors in Brazil filed corruption charges Wednesday against Luiz Inácio Lula da Silva, the former president who has wielded influence across Latin America for decades, portraying him as the mastermind of a sprawling graft scheme intended to maintain his party’s grip on the presidency.

Deltan Dallagnol, a prosecutor, called Mr. da Silva the “ultimate commander” of bribery and kickback schemes that allowed his leftist Workers’ Party to build coalitions in Congress, describing him as “the general” at the helm.

The actual charges against Mr. da Silva, who was president from 2003 to 2010, focus on a much narrower claim: Prosecutors accuse Mr. da Silva and his wife of illegally receiving about $1.1 million in improvements and expenses for a beachfront apartment paid for by a large construction company seeking public contracts.

But beyond the specific charges, which must still be accepted by a judge, the prosecutors said Mr. da Silva had been instrumental in a bigger corruption scheme that has thrown Brazil’s political system into turmoil for more than two years.