Jiri Dvorak, head of world governing body FIFA's medical services, said the players were not punished because they were not considered cases of doping but rather part of a big health problem in Mexico.
Dvorak said in a teleconference that "208 urine samples were collected during the (Under-17) World Cup and we analysed them in accredited WADA (World Anti-Doping Agency) laboratories," he said.
"It was an enormous surprise that 109 samples showed traces of clenbuterol, that means 52.4 percent of the players."
Mexican authorities have admitted the country has been affected by the practice of injecting cattle with the steroid, which is banned by WADA.
The players of the Mexico team that won the tournament tested negative because they had stuck to a diet of fish and vegetables.
"It's not a doping problem, it's a public health problem. When, in the first week of the tournament, we detected three cases and then another it was quite a surprise," Dvorak said.
Last week, WADA withdrew an appeal at the Court for Arbitration in Sport against the Mexican Football Federation's (FMF) decision not to sanction five senior players who tested positive for clenbuterol at the CONCACAF Gold Cup in the United States in June.
The FMF claimed the players had eaten beef contaminated by the steroid.
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