"I confirm that we have decided to end our partnership with the IAAF Kids Athletics programme with immediate effect," Nestle 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.
Nestle, the world's largest food company, became in 2012 the main sponsor of a programme aimed at promoting athletics for youths worldwide.
The IAAF is facing crises on multiple fronts, including widespread allegations of corruption and bribery under disgraced former boss Lamine Diack.
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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.
The head of the WADA commission, Dick Pound, said that Coe was almost certainly aware of widespread drug use within athletics, having served eight years as vice president under Diack.
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.
Speaking in Tokyo on Monday, Coe said "the journey back to trust is one of an uncertain length, but we have to make changes."
There was no immediate comment from the IAAF on Nestle's decision.