The Argentina attacker was crowned player of the tournament after his side lost the final 1-0 to Germany in extra time, but many fans and pundits have questioned that decision.
After popping up with a string of crucial goals during the group stage, Messi was below par throughout the knockout fixtures.
And Blatter conceded he was among those who were somewhat taken aback by the selection of Messi for the prize.
When asked for his take on the decision at a post-World Cup media conference, Blatter asked: "Shall I be diplomatic or shall I tell you the truth?
"Listen, I was myself a little bit surprised when I saw Messi coming up for best player of the tournament."
It was then suggested FIFA could look into changing the voting system for the award following this year's controversy over future tournaments in Russia and Qatar, but Blatter would not let it take the shine off an entertaining showpiece.
"It was a very special World Cup," he said. "What makes this World Cup so very special this time is the quality of the football and the intensity of the games.
"Naturally, when it came to the direct elimination matches, more tactics came into play, but there was not one single match that did not have this intensity.
"Every World Cup has its own history, but this World Cup on the field of play was exceptional.
"The bar has been set very high for the next World Cup [in Russia]."