Obama, during a visit to Argentina, revealed that his two teenage daughters Malia and Sasha were desperate to meet the Argentine international.
When questioned on the president's comments, Messi insisted that he would jump at the chance should the opportunity arise.
"Obviously, I was surprised that he said that, but on the contrary, for me it would be completely the opposite," Messi told TyC Sports. "For me it would be a source of great pride to be able to meet him and his daughters, but obviously I know it would be complicated.
"I don't know whether it is possible. Maybe he made the comment because he was in Argentina but I can say I was as surprised as everyone else."
Messi has scored 449 times in 520 appearances for Barcelona and has helped the Spanish club win seven La Liga titles and four Champions League trophies since 2004.