New Zealand have failed in their attempt to persuade the International Cricket Council to move their game against Kenya to South Africa.
Fleming's team have security fears
The Kiwis refused to travel to Nairobi for Friday's match, and the ICC's Executive Board has awarded the four points to the home side following a telephone conference to discuss the matter.
New Zealand Cricket officials have had security concerns about playing in Kenya since a bombing last November killed 16 people in Mombassa.
But they have decided not to appeal against the ICC decision.
Kenya's World Cup organising committee chairman Sharad Ghai described New Zealand's stance as "totally unjustified and was an insult to this country and its people".
He added: "We are happy for the points, but we would have liked to have played this match and not to have won them on technicalities."
There seemed little prospect of the game's governing body ruling in New Zealand's favour after refusing to move England's match in Zimbabwe to South Africa, and so it proved.
"I am happy that the matter is now resolved and that the ICC Cricket World Cup can move forward," said ICC chief executive Malcolm Speed.
"At the same time we have already seen some fantastic matches in this tournament and I am disappointed that this match will not be taking place."
Sri Lanka, meanwhile, have arrived in Nairobi, for their fixture on 24 February.
"We are glad to be here," captain Sanath Jayasuriya commented.
New Zealand must now win their remaining games against Bangladesh and Canada to try and clinch a place in the Super Six phase of the tournament.
They were beaten by Sri Lanka in their opening match, but bounced back with excellent wins over West Indies and hosts South Africa.