A commander in the Allied Democratic Forces (ADF) militia, Abdul Rashid Kyoto, alias Njovu, was captured earlier this month, and is also accused of leading a horrific massacre at a school in June.
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.
Prosecutors have "sanctioned two charges of terrorism, three charges of murder, three charges of aggravated robbery and one charge of belonging to a terrorist organisation" over the tourist attack, the director of public prosecutions said in a statement Monday.
A Briton and a South African were murdered along with their guide in an attack on October 17 while on safari in Queen Elizabeth National Park.
The IS group claimed responsibility, saying it had killed "three Christian tourists".
On Monday, Njovu "appeared before court and was remanded until November 27", Jaquelyn Okui, spokeswoman for the office of the director of public prosecutions, told AFP.
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 that Njovu was the only survivor of the operation.
The ADF is the deadliest of dozens of armed groups that plague troubled eastern Congo, accused of slaughtering thousands of civilians there, as well as carrying out cross-border attacks.
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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