Official says Lieutenant General Khoantle Motsomotso was shot by soldiers who had recently been fired.
Lesotho's army commander has been shot dead by rival military officers, according to the officials in the small southern African country.
Defence Minister Sentje Lebona confirmed the death of Lieutenant General Khoantle Motsomotso on Tuesday morning, The Associated Press news agency reported.
He was shot at his home by a group of soldiers who had recently been fired, said Ramanka Mokaloba, a defence official, according to DPA news agency.
"They attempted to forcefully enter his office. There was a shoot-out between the two... and the commander's bodyguards," another military official who declined to be named told AFP news agency.
At least one soldier was also killed during the attack and another injured.
Calls for government of national unity in Lesotho
Prime Minister Thomas Thabane confirmed the deaths at a press conference on Tuesday, describing them as "a serious setback to vigorous efforts to restore peace and stability".
Lesotho has been beset by power struggles and concerns about military interference in politics. The country has seen a number of high-profile assassinations, including the 2015 killing of a former army chief.
Thabane's party won elections in June, returning him to power three years after he fled Lesotho because of fears he was an assassination target.
Critics accuse the military of favouring Thabane's old rival Pakalitha Mosisili who ruled from 1998-2012 and 2015-2017.
Years of political friction have hampered attempts to fight dire poverty and the world's second highest HIV infection rate.