The 73-year-old believes the Barcelona star is still some way short of the Argentine and fellow Ballon d'Or favourite Cristiano Ronaldo and has defended Diego Costa's Brazil snub
In his first season with Barcelona, the 21-year-old has four goals and eight assists in 15 appearances, while the Argentina international has managed 12 goals and four assists in 14 matches.
Pele believes his compatriot has the potential to become one of the finest attackers in the modern game but feels he must be given time to develop in Europe before he can vie for the honour of being named the world's best.
"There are several good players, but the choice [for the Ballon d’Or] should be between Messi and Cristiano Ronaldo," he told reporters.
"I think Neymar can be the best player in the world, but there are players who are four or five years ahead, like Messi.
"Whether or not Neymar will become an idol in Barcelona is a question that I still can not answer, but I already said that I believe Neymar is one of the most complete players in the world.
"He does not have the experience of Messi or Cristiano Ronaldo, but is one of the best players in Brazil.
"However, eight months in Europe and in Barcelona will be good for Brazil because he will have more experience heading to the World Cup."
Pele also jumped to the defence of Diego Costa, insisting the player should be respected for making his reasons clear as to why he chose to represent Spain over Brazil.
"I think we have to respect the decision of Diego. He had a position and followed it. It was a beautiful attitude," the 73-year-old added.
"I understand he had to have courage to make the decision. He tried to explain that he had not been well received in the Brazilian national team and made the decision to represent Spain.
"I think that his attitude was correct. We have to respect it."