"I confirm that we have decided to end our partnership with the IAAF Kids Athletics programme with immediate effect," Nestlé spokeswoman Lydia Meziani told AFP in an email.
"This decision was taken in light of negative publicity associated with allegations of corruption and doping in sport made against the IAAF," she added.
Nestlé, the world's largest food company, became in 2012 the main sponsor of a programme aimed at promoting athletics for youths worldwide.
But Meziani said Nestle decided to "terminate (its) existing relationship with the IAAF" because a continued partnership "could negatively impact our reputation and image."
The IAAF is facing crises on multiple fronts, including widespread allegations of corruption and bribery under disgraced former boss Lamine Diack.
Separately, world athletics' new boss Sebastian Coe has faced criticism following Russia's ban from the sport for what a commission of the World Anti-Doping Agency's (WADA) described as "state-sponsored" doping.
WADA's report claimed that the IAAF governing council must have known about corruption orchestrated by Diack, and about doping in Russia.
Since the scandals broke, Coe has been travelling the globe, notably in Asia, where he has sought to shore up support for IAAF, hoping to ease the concerns of corporate backers weary of being tied to a tainted organisation.
Speaking in Tokyo on Monday, Coe said "the journey back to trust is one of an uncertain length, but we have to make changes."
Nestle said it had informed the Monaco-based IAAF of its decision and would "await a formal acknowledgement from them that our partnership has ended".
The defection of Switzerland-based Nestle as a sponsor came after the IAAF admitted last month that it was battling to retain corporate backing, amid reports that Adidas was also walking away.
The deal with the German sportswear giant signed in 2008 and reportedly worth tens of millions of dollars was due to run until 2019.
Independent investigations have found that corruption was embedded in the IAAF during the tenure of Diack, a Senegalese national now facing criminal charges in France.
There was no immediate comment from the IAAF on Nestle's decision.
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