Major General Dick Olum, the person tasked with overseeing the Uganda military operations against the ADF in the Democratic Republic of Congo, named the ringleader of the attacks as Abdul Rashid Kyoto, alias Njovu.
Njovu was captured in a raid late Tuesday.
Olum said the army had intelligence that Njovu also led an attack across the border in the DRC last week, which killed two Ugandan soldiers and two civilians.
"There is correlation (between) the three attacks and the command by Njovu," Olum said.
"We have a lot of intelligence about ADF. We know who has been carrying out these missions to kill people," he added.
The Ugandan military authority said the operation that led to Njovu's capture should reassure that nation and tourists that "Uganda is safe and ADF will be defeated."
The army on Thursday said it had detained the head of a unit of the ADF militia in an operation that killed six other fighters.
On the same day the army announced the detention of the ADF head, a Ugandan court sentenced seven people to between seven and 10 years in prison on a range of charges over their links to the militant group.
The defendants, including a 75-year-old man, had pleaded guilty to belonging to a "terrorist organization" as well as terrorism financing and child trafficking for recruitment into the ADF.
One also pleaded guilty to recruiting his own children into ADF ranks and to rape.
The East African nation alleges the ADF, which is affiliated with the Islamic State group, is responsible for the murder of the honeymooning tourists and their local guide in October, as well as the school attack that cost the lives of 42 people, most of them students.
Victims were hacked, shot and burned in the late-night raid on the school in Mpondwe, near the border with DRC — the worst such attack in Uganda since 2010.
The ADF is the deadliest of dozens of armed groups operating in the eastern DRC. It has been accused of slaughtering thousands of civilians and carrying out cross-border attacks.