The students who started their riot on Tuesday say the 15 percent cumulative increment, approved by the university council last year for privately sponsored students was unfair.
Teargas and live bullets were used to pursue the rowdy students, who are calling for the cancellation of the fees increment policy.
The army and Uganda police have maintained a heavy presence at the university to quell the protests.
Majority of the students have not turned up for lectures on Wednesday and those who had started their lectures were forced by the strikers to join the protest.
Among the arrested is the People Power Learning Guild president, Julius Kateregga and Ezra Byakutangaza, the University's Guild Speaker, among several other student leaders.
Both the Guild Speaker Ezra Byakutangaza and the Guild President Julius Kateregga were arrested while leading a procession of students in protest over Tuesday’s arrest of their colleagues.
Byakutangaza said they cannot accept the university management enforcing a tuition policy on the students’ fraternity before they are fully in agreement with them.
He added that the students were 'ambushed' by the policy, which was passed in the absence of meaningful consultation.
The arrested students have been charged with inciting violence.
Two other students have allegedly been handed letters of suspension from the university for allegedly inciting violence.
The suspension letters were delivered to the Police by Professor Eria Hisali, the Principal College of Business and Management Sciences and Gordon Murangira, the Personal Assistant to the Vice-Chancellor.
Around the same time last year, Makerere University suspended nine students for allegedly threatening to disrupt activities at the campus over tuition increment.