On Wednesday evening the food giant announced "We have decided to end our partnership with the IAAF Kids' Athletics programme with immediate effect".
It had reached this conclusion, it said, "in light of negative publicity associated with allegations of corruption and doping in sport made against the IAAF.
"We believe this could negatively impact our reputation and image and will therefore terminate our existing agreement with the IAAF, established in 2012."
At that time Nestlé saw the association as building on its Nestlé Healthy Kids Programme which focused on raising awareness of nutrition and health among school-age children.
The announcement came just two weeks after the BBC reported that Adidas ended a sponsorship deal with the governing body of international athletics on similar grounds.
IAAF president Sebastian Coe professed himself "angered and dismayed" by Nestlé's announcement. "We will not accept it," he declared. "It's the kids who will suffer."
The IAAF reported the Nestlé-sponsored programme had already been successful, with 15m 7-12 year olds in 76 countries taking part in team activities to promote a healthy, active lifestyle.
"In 2016, IAAF Kids' Athletics plans to reach a further 15 countries, training 360 lecturers, instructing 8,640 physical education teachers, with three million children participating by the end of the activation," it said.
Nestlé has had its share of criticism in the past as campaigners have taken it to task on a number of issues, ranging from promoting infant formula in places where clean water is unavailable to aiding the destruction of rainforests by using unsustainable sources of palm oil.
But according to Sigwatch, a group tracking NGO campaigns and the emerging issues driven by activists around the world, Nestlé was the most praised company on its watchlist in 2015, thanks to its efforts in tackling climate change, a commitment to zero deforestation, and its moves to clean up its supply chain.
Last November, for example, it volunteered the existence of slavery in its supply chain in Thailand, a step hailed as ground-breaking by several NGOs.
Data sourced from BBC, IAAF, Guardian; additional content by Warc staff