Rumours of Vincent Otti being murdered gain ground after his disappearance.
The reported split is the latest blow to the LRA which has waged a war in northern Uganda for 20 years.
Earlier this month, Joseph Kony, LRA’s leader, accused his deputy, Vincent Otti, of being a government spy and detained him in a Congolese forest hideout.
However, there is still speculation in Uganda that Kony had Otti killed.
The LRA has a history of executing commanders and fighters accused of spying.
Several fugitive LRA leaders including Kony and Otti are under intense pressure from war crimes indictments brought by the International Criminal Court.
Despite the LRA’s internal problems, Ayoo said the LRA remained committed to negotiations to end the fighting that has killed tens of thousands and uprooted nearly two million more.
The “internal affairs of LRA military, dismissal of or desertion by a few unruly … soldiers … will not deter to the LRA/M from delivering on its solemn commitment to pursue the Uganda peace talks,” Ayoo said.
Talks between the LRA and Kampala government are expected to resume in South Sudan next month.