The levels were consistent with meat contamination that had impacted dozens of athletes in Mexico over the last several years, they said.
As a result of the positive test, Golden Boy said Alvarez would immediately move his training camp to the United States from Mexico and submit to additional drug testing.
"I am an athlete who respects the sport and this surprises me and bothers me because it had never happened to me," said Alvarez.
"I will submit to all the tests that require me to clarify this embarrassing situation and I trust that at the end the truth will prevail."
Golden Boy said Daniel Eichner, the director of the World Anti-Doping Agency-accredited lab that conducted the tests, stated in a letter on Monday that, "These values are all within the range of what is expected from meat contamination."
At the 2011 under-17 soccer world championship held in Mexico, more than 100 players tested positive for clenbuterol, while the Mexican 2014 World Cup steered clear of beef in the run-up to the tournament due to fears about the substance.
Clenbuterol is sometimes illicitly mixed into livestock feed to make meat leaner.
Alvarez and Golovkin both agreed to be randomly tested by the Voluntary Anti-Doping Association as part of the deal for their initial fight last September and their rematch.
It was not clear whether Alvarez's positive test will affect the rematch.
Alvarez has a 49-1-2 record, with his only loss coming against Floyd Mayweather in 2013. His middleweight world title bout against Golovkin last September ended in a controversial draw.
(Reporting by Frank Pingue in Toronto; Editing by Peter Rutherford)
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