Assistant Inspector General of Police Andrew Kaweesi, who served as the force's spokesman and was one of the country's most high-profile officers, was killed on March 17 along with two other officers.
The suspects appeared before a magistrate's court in Kampala yesterday.
"The police arraigned 13 suspects before the court. They were charged with terrorism, murder and aggravated robbery," police spokesman Asan Kasingye told AFP.
They were remanded in custody until May 5, when they will reappear in court, he said, adding: "Inquiries are currently going on to apprehend other suspects who are still on the run."
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Kaweesi, protected by two officers who were also killed, was shot dead as he was leaving to go to work. A local resident described seeing four men on two motorbikes attack their car with what looked like AK47s.
Kaweesi rose to prominence as he spearheaded the police response to widespread opposition party protests following a controversial 2011 presidential election.
After a stint as commander of Kampala Metropolitan Police he was appointed director of operations and then head of human resources before assuming the role of main police spokesman in August 2016.
Kaweesi's killing resembles the assassinations of other high profile legal and military personnel.
In March 2015 Joan Kagezi, a senior public prosecutor, was shot in the street and the assailant escaped with an accomplice on a motorcycle.
In November last year Ugandan army officer, major Sulaiman Kiggundu -- a former Allied Democratic Forces rebel -- was shot in his car by gunmen travelling on two motorcycles. Both crimes remain unsolved.
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