German documentary maker Hajo Seppelt said "several" of the Caribbean island's athletes had traces of clenbuterol, a banned muscle-building substance, in recent re-tests of 8-year-old urine samples.
No athletes were identified. Jamaican sprinter Usain Bolt won three gold medals in world-record times and was the star of the Beijing Games.
The IOC said Monday it concluded there was no pattern of organized cheating, after consulting the World Anti-Doping Agency.
"After careful consideration, WADA informed the IOC further to the pattern analysis that the IOC had conducted that WADA could not find any significant and consistent pattern of abuse of clenbuterol in these cases and that it would be appropriate not to take these cases any further," the IOC said in a statement.
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China has a reputation for using clenbuterol in livestock farming to increase animals' muscle, and Olympic athletes were warned of contamination risks before going to Beijing. Without naming Jamaica, the IOC said the number of clenbuterol cases in the re-tests was widespread.
"During the re-analysis of the stored urine samples from the Olympic Games Beijing 2008, the laboratory found in a number of cases of athletes from a number of countries and from a number of different sports, very low levels of clenbuterol," the IOC said in a statement.
"We acknowledge that the clenbuterol meat contamination issue is unsatisfactory," WADA director general Olivier Niggli said in a WADA statement. "We will continue to invest in scientific research to try to solve this issue as quickly as possible."
Seppelt and German network ARD have consistently revealed and reported on doping scandals, including working with whistleblowers to expose systematic cheating in Russian track and field.
A Court for Arbitration for Sport panel judged that he did not intend to dope, and had ingested a contaminated supplement. Contador served a two-year ban and was stripped of the 2010 Tour win.