0328 GMT March 20, 2019
Botswana's Isaac Makwala, 30, had hoped to run in Tuesday's 400m final, but was barred from competing, BBC reported.
His country's Olympic boss, Falcon Sedimo, said that was "disturbing".
But the IAAF said it was under instruction to quarantine athletes who showed symptoms of the virus.
It acknowledged Makwala's absence was "a sad case" but said its medical staff examined the athlete and notes taken by a doctor showed he had been vomiting over an 18-hour period.
Pam Venning, head of medical at the IAAF, told BBC Sport, "I have to trust my doctors. My role is to ensure the healthcare of all the athletes here and it's a very infectious and very virulent disease."
In a later statement, the governing body said, "The team doctor, team leader and team physio had been informed following the medical examination that the athlete should be quarantined for 48 hours and would therefore be missing the 400m final on Tuesday."
Venning said "all the other teams" with affected athletes had adhered to IAAF instructions.
Makwala had been considered the main threat to Olympic champion and world record holder Wayde van Niekerk, who retained his world title by winning Tuesday's race.
The Botswanan earlier told BBC Sport he would be "devastated" to miss out as he was fit to race – having already been withdrawn from Monday's 200m heats.
But when he attempted to pass through the athletes' entrance to the stadium, an official and security personnel prevented him doing so.
'He's fit, he's well, he's prepared to run'
Public Health England said 30 athletes and support staff have been affected by sickness at the Tower Hotel in London – though the hotel is not the source of the outbreak.
The IAAF insisted it gave clear communication to the Botswana delegation that Makwala would not be allowed to run following a medical examination.
But Botswana officials said they had received no explanation as to why Makwala was not allowed entry, and had not been told to keep the runner in quarantine.
Sedimo told BBC Sport, "There has been no official communication, no formal communication from the IAAF at all. We found out from the media that he could not take part and he is heartbroken.
"There have been no medical tests at all, it's just generalized assumptions because of the outbreak of sickness and he has just one of those symptoms."
Botswana medical team member Simon O'Brien said Makwala showed no symptoms of the bug and blamed "poor communication" from the IAAF for the athlete missing the race.
"He's fit, he's very well, he's prepared to run, and he's just being kept away by the IAAF," said O'Brien, who insisted there was no sign of the illness during the time he spent with Makwala.
Some athletes have questioned the decision.
After winning gold, Van Niekerk said, "I would love him to have his fair opportunity. I believe he would have done very very well. I've got so much sympathy. I really wish I could give him my medal."
Who else has been affected?
Several German and Canadian athletes staying at the Tower Hotel fell ill last week.
A further 30 Germans due to arrive on Tuesday were moved to other hotels.
German triple jumper Neele Eckhardt collapsed but was well enough to compete on Saturday, and took part in Monday's final.
The Ireland team, which is also staying at the hotel, confirmed that one athlete – 400m hurdler Thomas Barr – has been affected.
The Tower Hotel said investigations conducted with environmental health officers and the IAAF had shown the hotel was "not the source of the illness". That has also been confirmed by Public Health England.