"We have issued arrest warrants for six people," said Director of Public Prosecutions Richard Buteera.
Buteera listed the six wanted leaders of the Movement for the Restoration of the Ten Commandments of God as Joseph Kibwetere, the movement's "prophet", Credonia Mwerinde, its so-called "programmer", Dominic Kataribaabo, a former Roman Catholic priest, and three others whom Buteera named only as Kasaburari, Kamagari and Komuhangi.
The warrants are linked to charges of 10 counts of murder, he said.
"This is 10 counts for now, but it could be more," said Buteera. "The investigations are still going on. This is not the last charge. This is really a holding charge, we shall eventually have the proper charge.
"If they are arrested eventually, when the investigations are complete, then the proper charge shall be preferred," he added.
Around 400 members of the cult died March 17 in a fire in their church in the southwestern village of Kanungu. Since then, the bodies of hundreds of other people, many of them women and children, have been found buried on properties linked to members of the cult.
Erasmus Opio, director of the police's Criminal Investigations Department, told AFP on Thursday, "we believe they are alive. That's why we went for arrest warrants.
"We are looking for them both within the country and outside, but there is no lead so far as to their whereabouts."
Police had previously claimed that Kataribaabo had died in the Kanungu blaze, saying his body had been found close to the church's exit, as if he had been trying to escape.
"There is no evidence to prove that was Father Kataribaabo's body, so it is possible he is alive," said Opio.
"We have already communicated to Interpol. Immediately you have arrest warrants you are authorised to get the assistance of international police," he said.
"These are international warrants of arrest. So with this authority from court, all countries are now going to look for them," he said.