Gunmen attacked the Maseru home of Lieutenant-General Maaparankoe Mahao, district police commissioner Mofokeng Kolo confirmed, deepening a seeming battle for control of the military.
The pre-dawn attack was reportedly unsuccessful, killing only a dog, but Mahao’s whereabouts is now unknown.
Mahao had been appointed head of the Lesotho Defence Force by prime minister Tom Thabane shortly before he was forced to flee to South Africa in the early hours of Saturday morning.
Previous commander Lieutenant-General Tlali Kamoli was accused of leading a coup attempt against him, a charge the military denies.
Low-ranking soldiers said it was unclear who was now giving their orders. They remain confined to barracks.
As some life returned to Lesotho’s streets on Sunday, it was not clear who was in charge of this beautiful but poor mountainous kingdom of two million people.
Thabane is across the South African border in Ladybrand, unable or unwilling to return.
“I have been removed from control not by the people but by the armed forces and that is illegal,” he said.
Meanwhile, Deputy Prime Minister Mothejoa Metsing told AFP he left Lesotho for talks in Pretoria.
“It is through the invitation of the South African president,” who currently heads regional bloc the Southern African Development Community’s security committee, Metsing said.
“There is no coup in Lesotho,” he insisted.
In the absence of the premier and his deputy, constitutionally, the Minister of Public Service Motloheloa Phooko is in charge of the kingdom, he added.
Phooko is a member of Metsing’s Lesotho Congress for Democracy party, which was in an uneasy coalition government with Thabane.
The party has also denied allegations of involvement in the coup.
Police struggled to regroup after a deadly attack by the military on key installations on Saturday, which resulted in an arsenal of weapons being seized.
District police commissioner Mofokeng Kolo confirmed that one officer died in the attack.
Twenty-four hours later the police headquarters was still abandoned and most officers remained in hiding.
Amid the political turmoil, Maseru’s residents stocked up on food and basic necessities.
“People are worried what will happen, because ‘no work, no pay’,” said fruit and vegetable vendor Kamele Pakisi. “There is no stability.”
Worshippers filled the city’s cathedral as normal but many feared for what lies ahead, convinced this spasm of political violence was not yet over.
There is concern that a mass anti-government demonstration that was planned for Monday could bring a new chapter of violence.
“We are not afraid of today, we are just afraid of tomorrow,” said Mphasa Chonela.
The police have called for the march not to go ahead, but critics question whether that is an attempt to protect the prime minister from criticism.
Lesotho’s neighbour, regional power South Africa and the Commonwealth warned the Lesotho Defence Forces that such action “shall not be tolerated”.
The United States voiced concern at the security clashes and called for “peaceful dialogue” in Lesotho.
Lesotho has suffered a series of coups since independence in 1966 and the political temperature in the country has been rising rapidly in recent months.
The prime minister suspended Parliament in June, forcing divisions in the ruling coalition to the fore.
South Africa has backed Thabane and could yet decide to intervene directly to return him to power.
In 1998 South Africa launched an ill-fated invasion of Lesotho when the “kingdom in the sky” was in the midst of another political crisis, reducing the capital to rubble. – Sapa-AFP