World Athletics says two employees and a contractor stole €1.5m (£1.3m) of its money as part of a "systematic theft" that lasted several years.
The sport's international governing body said one of the employees and a consultant had been sacked following an internal investigation, while the other had already left the company.
It said just over €1.5m (£1.3m) was stolen.
The theft was uncovered by the body's finance department during its first annual auditing process, under a new financial team.
World Athletics said detailed cases were handed over to judicial and legal authorities for criminal investigation.
It added that "a set of enhanced internal financial controls" will be introduced to prevent future frauds.
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'It is important we do the right thing'
Sebastian Coe, the World Athletics president, said: "Unfortunately, corporate theft happens in organisations around the world and across all industry sectors at different levels.
"The most important thing is to identify it, review how it was able to happen and then introduce new processes and enhanced controls to ensure it doesn't happen again. This is what we have done.
"We are also determined to recover whatever monies we are able to using the full force of the law to do this.
"Too many organisations brush incidents like this under the carpet, terminating employment with limited information which allows perpetrators to continue their scams and thefts within new organisations. We are not that type of organisation.
"We have built a strong reputation for good governance, transparency and for defending what is right, even if it is sometimes a little uncomfortable.
"This is uncomfortable but it is important that we do the right thing."
(c) Sky News 2025: World Athletics blames employees for £1.3m taken in 'systematic theft'
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