DeKalb County police say they've verified that Concepcion Cruz boarded a flight at the Atlanta airport bound for El Salvador on Tuesday.
Officials earlier said the 57-year-old man had been put on the no-fly list.
Police say Cruz is charged with two counts of felony hit-and-run in a crash that killed 2-year-old Caleb Lindsey on April 5.
Authorities say the boy, his sister and their mother were standing outside a Walmart in Tucker when they were hit by a white pickup truck. Their mother wasn't injured, but the girl was hurt.
DeKalb police say federal authorities and the government in El Salvador are working to locate Cruz.
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