"I had to choose somebody else, knowing that Lionel Messi is the best player in the world," the Argentina coach told reporters, adding that he had voted for Manchester United and Portugal forward Cristiano Ronaldo instead.
Maradona said the rules banned coaches from voting for players from their own country.
"Whoever thought that up is stupid," he said. "It's incredible, I voted for Ronaldo when I wanted to vote for Messi but I couldn't."
Ronaldo was named FIFA World Player of the Year at a ceremony on Monday while Messi was second, with Liverpool and Spain striker Fernando Torres third.
The FIFA award is based on votes by the national team coaches and captains of the 208 member associations of world soccer's governing body.
Maradona was speaking after a two-week trip around Europe in which he visited a number of Argentina's top players, their clubs and coaches.
Maradona heaped praise on Inter Milan coach Jose Mourinho. "He's a sensational person," he said of the Portuguese. "He's somebody I look up to."
Maradona also thanked Barcelona president Joan Laporta and coach Pep Guardiola, saying they had agreed to release Messi for the friendly against France on February 11.
"They behaved like gentlemen and opened Barcelona's doors to me after a long time," he said. "Laporta and myself want the best for Messi."
Last year, Argentina agreed not to select for Messi for friendly internationals after Barcelona agreed to let him take part in the Olympic Games.
The France game will be Maradona's second in charge after his surprise appointment. He began with a 1-0 win away to Scotland in November.
