Motomoto was allegedly shot by Brigadier Bulane Sechele and Colonel Tefo Hashatsi on Tuesday.
The two are alleged to have later been killed by Motomoto’s bodyguards.
The deaths of the three soldiers were confirmed by Lesotho Prime Minister Thomas Thabane on the same day.
Analysts say the killings reflect the instability that has plagued the country since the army rebellion of 2014, known as the failed coup.
They say the killings occurred because those who were involved in the rebellion and murder of then-commander Maaparankoe Mahao in 2015 could see that the net was closing in on them as the government moved to implement Southern African Development Community (SADC) recommendations.
Professor Mafa Sejanamane of the National University of Lesotho says the army rebellion was never suppressed.
Instead, when prime minister Pakalitha Mosisili’s 2015 administration came into office “it embraced the rebellion and went on with that”.
This was corroborated by Dr Tlohang Letsie from the department of political and administrative studies of the same university, who understands the killings were orchestrated by protracted divisions and rebellion within the army.
He said the incident had intensified the need for the swift execution of the SADC decisions aimed at restoring peace and stability in Lesotho.
Following the killing of Mahao, an SADC commission of inquiry, led by retired Botswana Justice Mpaphi Phumaphi, made recommendations that were acceded to by the SADC Summit that soldiers fingered in the killing of Mahao and others who committed several other crimes that included treason, murder and attempted murder must be prosecuted.
Sechele and Hashatsi were among the soldiers recommended for prosecution.
Letsie said their killing would speed up the recommendations because they had been partly self-implemented by their deaths.
“This has shown that those recommendations were long overdue,” he said. “My understanding is that the SADC fact-finding mission that includes security chiefs will help quicken the implementations than the pace the government thought it would do on its own.
“On the basis of political developments in Lesotho lately, the incident had an element of a coup, I don’t think the fighting would just end within the army if the perpetrators were not also gunned to death.
“These are the very same people that some of our political leaders (Mosisili and former deputy prime minister Mothetjoa Metsing) said they were able to remain in power only because of their support and have to be defended,” said Letsie.
He said now that Mosisili and Metsing were relegated to the opposition, the mutiny would have advanced into a coup.
“I definitely see a link; this uprising would have extended to the government if it was successful. You can’t have those people who are hostile to the incumbent government in the barracks as it is committed towards restoring rule of law.”
Letsie backed Thabane and said the army was under civilian control as the killings were contained within the barracks and did not spiral out or affect pillars of government.
He said Thabane was talking about the army as an institution that was seen to be having rogue or rebellious elements and was trying to show that the larger part was under control.
Sejanamane, on the other hand, has warned: “If the government hesitates to act, more trouble shall come, but if the government acts decisively and asks the SADC to support them, they should be able to keep the lead on this thing.”
He also urged the regional body to prove itself and act decisively on Lesotho’s security instability.
Sejanamane said the contention was that the Thabane-led government has just come into office and proclaimed it would implement the SADC decisions.
But, he said the killing of yet another army commander came “in panic”, as the suspects “wanted to disrupt the whole process because it was clear they could not stage a coup”.
The only thing which they could do was to kill people.
"It was an assassination and nothing more than that,” Sejanamane said.
He argued that during Mosisili's administration the army had been turned into a militia, and the Thabane administration had delayed bringing in the SADC to reinforce its early warning mechanism with necessary resources.
The delay had “allowed the militia time to think how best to disrupt the whole process of disbanding them”.
Sejanamane said he was confident that Thabane’s administration was determined to dismantle the militia but was delayed in doing it.
“They killed an army commander who was installed recently and was begging to accept and respond to the authority of the government,” he said. - MNN Centre for Investigative Journalism