The under-21 team lost their 11/12th place playoff match to Samoa 27-64 on Sunday (CI time) to finish outside their top 10 target.
The Baby Black Pearls had a good start to their campaign after a close 41-43 loss to Jamaica followed by 41-50 and 39-52 defeats to Botswana and Uganda, respectively.
In the final group match, the national team was held to a 45-all draw by the Malaysians.
Cook Islands recorded their first win of the tournament on Wednesday last week, beating Trinidad and Tobago 40-31 to progress into the 9-12th place playoff in which they went down to Zimbabwe 41-55 before losing to Samoa.
The team was reportedly plagued by illness throughout their three-week stay in Gaborone, with players struck down by two separate viruses.
In an interview with Radio New Zealand Cook Islands head coach John Glassie said they were never able to play a match at full strength.
“I’m so proud of the girls the way they fought, even though they were sick,” he said.
“We had girls on a drip visiting the doctor in the morning and then rocking up for the game in the afternoon.
“The fact that they could still keep fighting and keep going to the very last minute of the game that’s just a testament of their toughness and what they wanted to do for the Cook Islands.
“Yes we finished 12th – it’s not where we wanted to finish – but under the circumstances I think that it’s probably a very good result for us.”
The Samoans were outclassed by eventual champions New Zealand in their opening game, but went on to win four of seven matches.
Samoa head coach Lee Edwards said the players got better as the tournament went on.
“Obviously we had a couple of close losses (by two goals against both Scotland and Botswana), which set them back from their goal of making the top eight but I’m really proud of how they finished in the final game against the Cook Islands,” Edwards said.
Fiji recorded the top finish from the Pacific after managing the fourth place.
The team was thrashed 70-35 by England in the playoff for bronze medal.
Meanwhile, New Zealand defended the title, beating Australia 60-57 in the final.
- Rashneel Kumar/Radio New Zealand