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Lord Coe has vowed the IAAF will not accept a decision by food giant Nestle to abruptly terminate its sponsorship deal with world athletics' governing body.
Swiss-based Nestle said on Wednesday it was concerned its own reputation could be damaged by association, owing to doping and corruption scandals involving the IAAF, and would be immediately withdrawing its financial backing.
Nestle supports the IAAF Kids' Athletics programme, being its main sponsor since agreeing a five-year deal that took effect in January 2012 and has just entered its last year.
It is understood to have been paying around one million dollars (?690,000) per year but has asked the IAAF to immediately remove all Nestle branding from its website.
The IAAF said the programme is due to benefit three million children in 2016, but needs the sponsorship funding.
IAAF president Coe said in a short statement on Wednesday night: "Angered and dismayed by today's kids' athletics announcement. We will not accept it. It's the kids who will suffer."
Nestle's move came as a new setback to the governing body and Coe, who was elected as president last August and has since seen the reputation of the IAAF suffer repeated blows.
The IAAF was understood to be preparing a legal challenge.
Nestle said in a statement: "We have decided to end our partnership with the IAAF Kids' Athletics programme with immediate effect. This decision was taken 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."
The IAAF first responded by saying it was "in discussion" with Nestle over the final year of the contract.
Coe's later involvement served to demonstrate the IAAF's determination to save the deal.
The IAAF said its programme had so far involved 15 million children aged from seven to 12 years old. It said that Kids' Athletics, with Nestle's funding, planned to reach 15 more countries in 2016, training 360 lecturers and 8,640 physical education teachers.
That is now under threat, as the IAAF battles to cling to its blue-chip sponsor.
Last month it emerged that German sportswear giant adidas was looking to end its deal as a leading sponsor of the IAAF four years early.
Athletics is reeling from two damning reports by the World Anti-Doping Agency's (WADA) independent commission which revealed ''state-sponsored'' doping in Russia and raised questions about widespread doping in other countries.
Life bans were last month handed to Papa Massata Diack, who is the son of former IAAF president Lamine Diack and was a marketing consultant for the organisation, together with former Russian athletics federation (ARAF) president and IAAF treasurer Valentin Balakhnichev, and Alexei Melnikov, a senior ARAF coach. All three have appealed against the sanctions to the Court of Arbitration for Sport.
The IAAF's ethics commission found the trio had blackmailed Russian Liliya Shobukhova, the London marathon winner in 2010, and made her pay a bribe for a positive drugs test to be covered up.