Maatougui covered the distance in 3h36mn44s and earned the green jersey.
Moise Mugisha of Rwanda came second (3h36'46"), ahead of his compatriot Jean Claude Nzafashwanayo.
French cyclist Vincent Graczyk of the Club de la défense is the current holder of the yellow jersey.
For his part, Morocco's Anass Ait El Abdia ranked 6th in this 3rd stage.
About 60 athletes from 10 teams representing Ivory Coast, Nigeria, DRC, Morocco, Senegal, France, Rwanda, Cameroon, and Burkina Faso are taking part in the 18th edition of the International Cycling Tour of Cameroon which runs until June 12.
Morocco participates in this tour with 6 cyclists namely Adil Al-Arbaoui, Anas Ait El Abdia, Mounir Makhchoun, Sabbahi El Houcaine, Nasr Eddine Maatougui, and Ashraf Ed Doghmy.
The Moroccan selection is supervised by coach Abdelati Saadoune.