"Neymar, I hope you recover very soon friend!," wrote the Argentinian on his Facebook page alongside a photo of the two stars in their Barcelona jerseys.
Brazil and Argentina are the fiercest of rivals, but Messi, 27, clearly cares for Neymar, having played with the 22-year-old at club level for the past year.
Argentine football great Diego Maradona also lamented Neymar's injury.
He told Venezuela-based Telesur TV network: "It concerns not only the Brazilian people but all of us who love football. It was his World Cup, in his country. He had great hopes."