The agency has also slapped a penalty of Rs. 15 lakh each on Khan, who sings for Bollywood movies, and Ali.
The duo, whose passports are with the DRI, will be allowed to leave the country after depositing the penalty.
"Diaries seized from Rahat's event manager Chitresh Srivastava had mentioned payments to the sufi singer during his trip to India last year. Rahat had then smuggled out around $80,000 from India," a source said.
When Khan, Ali and Srivastava were confronted with these diaries, the singer admitted to smuggling money last year too, the source said.