CAF acted after medical examinations conducted on the players showed they are above the cut-off age set for competing in this age-group tournament.
The youth competition kicked off in Dar es Salaam on Saturday and will be used to determine which teams compete at the Africa Cup of Nations next year, and later on the Fifa U-17 World Cup.
An MRI scan by the Confederation of Africa Football nabbed Lesley Otieno, Maxwell Mullili and Abdulmalik Hussein Abdallah – all found to be above the required age bracket.
This comes in the wake of Football Kenya Federation having conducted a similar exercise before the team departed for Tanzania.
Caf Vice-President of Medical Committee, Yacine Zerguini also sent home three Ugandan players; Kafumbe Joseph, Elvis Ngonde and Oluka George, while host Tanzania had two over-age players are Fred Chande and Jafary Mtoo.
None of the six participating countries were spared in the attempted age-cheating scheme by the Cecafa regional members.
The regional games to kicked-off on Saturday with the winner grabbing a ticket to the U-17 Africa Nations Champions to be held in Tanzania.