The 29 year-old stunningly announced he was set to retire from internationals after his side's penalty shoot-out loss to Chile in the Copa America Centenario final on Monday (AEST).
Fans and players have urged Messi, Argentina's all-time leading goalscorer, to reconsider.
Marci has tried to do the same and said the Barcelona star was huge for the country.
"I spoke with him to congratulate him and tell him he had done a great championship," Macri told reporters.
He added: "I don't understand. The truth is that it's a joy, a gift from God, to have the best player in the world in a country like ours.
"Messi is the biggest thing we have in Argentina, so you have to take care of him."
Macri spoke to Messi on Monday, a day after Gerardo Martino's men went down to Chile 4-2 on penalties.
He also wanted the miraculous attacker to ignore critics, saying: "I told him not to pay attention to all the comments being made because, in truth, we are very happy."
Messi scored five goals at the Copa, but he put his penalty in the shoot-out over the bar as Argentina's 23-year trophy drought continued.
He is yet to speak publicly since announcing his decision.