A statement released by Uganda's director of public prosecutions said Kyoto, alias Njovu, was sanctioned with "two charges of terrorism, three charges of murder, three charges of aggravated robbery and one charge of belonging to a terrorist organization."
The ADF commander was facing allegations of killing a Briton, a South African and an Ugandan tour guide on October 17 where they were on safari in Queen Elizabeth National Park.
Uganda has blamed the ADF, which is affiliated with the Islamic State group, for the murder of the honeymooning tourists and their local guide, as well as the school attack that cost the lives of 42 people, most of them students.
The IS group claimed responsibility, saying it had killed "three Christian tourists."
Prosecutors said Njovu was arrested on Lake Edward, which straddles the border with the Democratic Republic of Congo, with two of his associates shot dead while "others managed to escape in a boat with their weapons."
The army had earlier said he was the only survivor of the operation.
After the October attack, President Yoweri Museveni called on the security forces to ensure the ADF was "wiped out" and the military has carried out a number of air strikes against its positions in the DRC.
The ADF is historically a Ugandan rebel coalition whose biggest group comprised Muslims opposed to Museveni.
Britain has advised its nationals to avoid travel to certain areas of Uganda, including the Queen Elizabeth park.
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