Coach John Glassie said the illness affected the performance of the team which lost its opening two pool matches over the weekend.
The Baby Black Pearls lost their opening group match to giants Jamaica 43-41, before losing to hosts Botswana 51-41.
Against the Jamaicans, the national team blew a five goal advantage to concede the close loss.
Glassie said nine of their 12 players had been hit with the bug, which has been lingering for more than a week.
He said the team have moved accommodation in recent days, and managers are monitoring closely what food the players are eating.
“It’s still a bit there, a few of the players are still suffering from it but we’ve been trying to deal with it,” Glassie told Radio New Zealand.
“We ran out of medication after four days so we’ve been going to the event with doctors getting more medication every couple of days.
“So the girls are getting better but obviously not being able to hold food down and that sort of thing does play a part in preparation. So that’s why these physical games are taking such a toll on the players.” Glassie said the vocal home crowd played a major part in the team’s second loss.
“With Botswana the major factor, there would have been a large crowd and after seeing briefly the live footage it’s hard to comprehend how loud the crowd actually is.
“Just being able to talk to the players and that sort of thing - we’re trying to yell out during the breaks - and even talking to my assistant coach next to me we had to yell at each other because it was deafening.
“They had a great support from their home-based crowd and it really did make a difference. The girls said it was very hard to concentrate it was so loud; it was deafening at some stages.”
Cook Islands played Uganda in its third group match late yesterday before taking on Malaysia in the final match today.
The team is all but out of the final playoffs. - RK/RNZ