A store owned by the relatives of Messi, who led Argentina to victory at last year's World Cup, was gunned down.
Ripples are spreading locally because documents that threaten Messi players were also left.
A supermarket run by Messi's wife's family was shot by someone in Rosario, the hometown of Messi, who led Argentina to its first World Cup victory in 36 years last year.
No one was injured by the shooting, and a handwritten document was left at the scene threatening Messi, saying, "I'm waiting for you."
Local media said two men, believed to be linked to a drug cartel, appeared on motorcycles and fired at least 14 shots into the store.
Rosario, who spent until the age of 13 when Messi moved to Spain's prestigious Barcelona, is known for many drug-related crimes in Argentina.
President Fernandez has called on local mayors to expedite their response to rising crime.
Ripples are spreading locally in the situation where relatives of Messi, who has become a national hero by winning the World Cup, are damaged.