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During his regular radio broadcast, following the footballer's arrival in the capital Montevideo Friday, Mujica said: "The disciplinary measures against Suarez were a monstrous aggression, not just against a man, but also against a country".
"We'll never understand the truculence, the form, the procedures applied, against Suarez," Xinhua quoted Mujica as saying.
The disciplinary committee of football's governing body FIFA suspended Suarez from playing in nine competitive international matches, banned him from any football-related activity for four months, and fined him 112,000 dollars.
FIFA said Suarez bit Italian defender Giorgio Chiellini during a group phase match that Uruguay won 1-0, eliminating the Italians from the cup.
The incident marks the third time Suarez has been penalized by FIFA for biting an opponent on the field, but this time the penalty has greater repercussions, since it prevents him from taking part in any of the remaining World Cup matches.
"The penalty will forever be an embarrassment in the history of the World Cup," said Mujica.
"He is a boy genius whose intelligence is in his feet. (He is) brilliant on the field, he couldn't stand a moment of over excitement, he couldn't stand it and he exploded," Mujica said of the biting incident.
Mujica said: "I was at the airport at 5:30 am with his family to welcome him, on a cold morning but with a warm heart, and in the middle of the airstrip I gave him a humble hug and invited him to continue living and struggling."
"I tried to be a symbol for the affection of the Uruguayan people, which under these circumstances don't judge, they surround you with affection," said Mujica.
The castigated national team forward landed at Montevideo's Carrasco International Airport and headed straight home to Ciudad de la Costa, near the capital Montevideo.
Hundreds of football fans had converged on the airport Thursday evening, when Suarez was originally scheduled to arrive, but as his flight was delayed, fans gradually left the building.