Coe, head of the International Association of Athletics Federations (IAAF), told the BBC on Tuesday: “I did not lobby anyone on behalf of the Eugene 2021 bid” in the US state of Oregon.
Nike started out in Eugene and is now based in Beaverton in the same state.
Eugene was awarded the event without a bidding process, despite strong interest from the Swedish city of Gothenburg.
“The situation was unusual but not unprecedented. A bid process did not take place when Osaka was awarded the 2007 World Championships,” Coe said.
“The process for bidding is already being reviewed as part of a wide range of reforms currently being prepared,” he added.
The defence came following a BBC investigation.
After being shown emails claiming that Coe contacted then-IAAF president Lamine Diack to support Eugene’s bid, Bjorn Eriksson, head of Gothenburg’s failed 2021 bid, told the BBC: “It doesn’t look good at all.
“It smells and it has to be investigated. That’s for the sport, for everybody involved,” he said.
Coe, who reportedly earns $A138,000 a year in his role as ambassador for Nike, was an IAAF vice president at the time.
Coe was elected president of the IAAF in August after spending eight years as deputy to Diack, who is being investigated by French police on suspicion of having taken more than one million euros in payments to cover up positive drug tests.
The timing of the allegations of Coe’s conflict of interest is not great for either the former two-time Olympic 1500m champion or the IAAF.
The IAAF Council meets in Monaco on Thursday to discuss Russian track and field, just three weeks after deciding to temporarily suspend one of the sport’s powerhouses.
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