The allegations, by an unnamed insider, were broadcast by the BBC on their Newsnight program on Thursday and reported on the website www.bbc.co.uk.
"Any suggestion the loan was made in return for promises of gold medals at the 2012 Olympics is preposterous and utterly untrue," said an AIBA statement on the BBC's website.
The BBC said it had uncovered evidence of "secret payments" of millions of dollars from a mystery source in Azerbaijan to World Series Boxing (WSB), a competition run under the auspices of the AIBA.
"It was an arm's length transaction between two entities made on a commercial basis and with a view to a commercial return for the investor," the statement added.
"While that investor prefers not to be named ... AIBA/WSB can confirm that they are a private investor and are not the Azerbaijani Government," the statement added.
"AIBA/WSB believe that such allegations have been made by individuals with an axe to grind, who are totally discredited.
"As well as unjustifiably imputing corruption to AIBA/WSB, they demonstrate a complete misunderstanding of the procedures which lead to the award of Olympic boxing medals and the impossibility of influencing these."
AIBA has already announced that London 2012 will have a new electronic scoring system, making each ringside judge openly accountable for his actions.
There were fears at the last Games in Beijing the boxing competition was open to manipulation.
He described the allegations as "totally impossible and ridiculous" but said he would probe any wrongdoing.
"Thanks for informing about this information, I will immediately conduct an investigation," he told the broadcaster.
(Reporting by Alan Baldwin, additional reporting by Ossian Shine; editing by Martyn Herman and Alastair Himmer)
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