Most of the senior players, led by their former captain Steve Tikolo, refused to attend training on Tuesday and Wednesday as a result of the dispute.
Subsequently Tikolo and eight other players who did duty for Kenya in the ICC Champions Trophy in England were dropped from the provisional team of 15 selected late Wednesday.
"We have to go by the players we have been given to select," the Kenya Cricket Association chief selector Harilal Shah told AFP.
Left arm batsman Hitesh Modi, one of the five senior players in the squad, was named as the new captain to lead the relatively young team for the three-day match against the Namibians.
Shah said the final team of 12 will be selected on Thursday after the final practice session.