The 26-year-old was seen doubled over just minutes before scoring in the friendly win over Slovenia and his coach believes the problem is because of nerves.
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The Barcelona ace was seen vomiting during an international clash with Bolivia and has since done the same in a handful of appearances, including Argentina's latest friendly against Slovenia, in which he scored just four minutes later.
After Messi threw up in a friendly match between the Albiceleste and Romania in March, former Barca coach Gerardo Martino admitted that "something is not right" though he added that he did not believe Messi's play was being affected.
And Sabella has now claimed the problem is as a result of nervousness on the part of the 26-year-old.
"Nerves. I reckon that in these moments there is anxiety more than anything," Sabella said ahead of his team's departure for Brazil. "It's difficult to remain calm."
Neither Barcelona nor Argentina's team doctors have found a medical cause behind the problem, but Messi himself is convinced it is something that happens and cannot be avoided.
"I don't know what it is. But I had a thousand exams," Messi told the Argentine broadcaster TyC Sports earlier this year. "I start to feel nauseous to the point where I almost vomit, and then it goes away."
Messi, who left his homeland at the age of 13 to join Barcelona's La Masia academy, has also admitted to being affected by a common view that he does not give his all for the national side.
"Argentina is my country, my family, my way of expressing myself," he recently told Marca. "I would change all my records to make the people in my country happy."
Argentina has been drawn in Group F alongside Bosnia-Herzegovina, Iran and Nigeria.
Their first game will be against Bosnia-Herzegovina in Rio de Janeiro on June 15, before it faces Iran in Belo Horizonte on June 21 and Nigeria in Porto Alegre on June 25.