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The Swiss-based food and beverage company has sponsored the IAAF's Kids Athletics programme since 2012.
But Nestle have followed Adidas' lead in cutting ties with the IAAF, who have been accused of covering up doping in athletics.
"We have decided to end our partnership with the IAAF Kids Athletics programme with immediate effect," a Nestle statement read.
"This decision was taken in light of negative publicity associated with allegations of corruption and doping in sport made against the IAAF.
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"We believe this could negatively impact our reputation and image and will therefore terminate our existing agreement with the IAAF, established in 2012.
"We have informed the IAAF of our decision and await a formal acknowledgment from them that our partnership has ended."
The IAAF subsequently released a statement seeming to contradict that of Nestle, suggesting the organisations had not severed their agreement, and underlining the reach of the Kids Athletics programme.
It read: "The IAAF is in discussion with Nestle concerning the final year of its five year partnership with IAAF Kids’ Athletics.
"This has been a successful programme with 15 million kids aged 7 to 12 years in 76 countries taking part in fun team activities which promotes a healthy, active life style.
"In 2016 IAAF Kids’ Athletics plans to reach a further 15 countries, training 360 lecturers, instructing 8640 Physical Education teachers, with three million children participating by the end of the activation."
Last month, sports branding giant Adidas said it was in "close contact" with the IAAF amid reports the German company had ended its sponsorship deal with the governing body four years early.
However, both Dentsu and Canon have indicated they have no intention of ending their respective partnerships with the IAAF.