This reportedly forced the prime minister to flee the country.
Metsing took charge of the government once Thabane had fled the country for neighbouring South Africa. Thabane left on Saturday, after the army surrounded his residence and police stations in Lesotho's capital, Maseru.
(READ MORE: Gunfire heard in Lesotho, diplomats report apparent coup attempt)
Gunshots were heard in Maseru on Saturday, where one policeman was shot dead and four others wounded, said senior police superintendent Mofokeng Kolo. But the army denied trying to force out Thabane, saying it had moved against police suspected of planning to arm a political faction in the small southern African kingdom.
Diplomats in Maseru told Reuters the army was largely seen as loyal to the deputy prime minister and the police force mostly supported the prime minister.
Regional power South Africa condemned the army’s actions and invited the deputy prime minister to talks there on Sunday, Lesotho's Minister of Communications, Science and Technology, Selibe Mochoboroane, told Reuters. He did not specify who the talks would be with.
“Constitutionally, in the absence of the prime minister, the deputy prime minister takes the reins,” said Mochoboroane, who is also spokesman for Metsing's party.
“For now there hasn’t been any arrangement, but it goes without saying the deputy prime minister will still oversee other issues that need to be taken care of until the prime minister returns,” he added. On Saturday, Mochoboroane echoed the army’s assurance that no coup had taken place.
The prime minister, who expected to be back in Maseru in two days time, said he believed his deputy was behind the plans for a coup. The two would not be holding talks in South Africa, he said.
“I have no much reason to absolve him from blame,” Thabane told Reuters. “Looking from a distance, he is very active in this show.”
Relations have been stormy between Thabane’s All Basotho Convention party and Metsing’s Lesotho Congress for Democracy (LCD) group, which formed a coalition with another party after elections in 2012.
Thabane dissolved parliament in June to avoid a no-confidence vote against him amid feuding among the ruling parties. Metsing later said he would form a new coalition that would oust Thabane.
The African Union said on Sunday it would not tolerate any illegal seizure of power.
Thabane told Reuters on Saturday he had fired an army commander, Lieutenant-General Kennedy Tlali Kamoli, and appointed Brigadier Maaparankoe Mahao to replace him. But on Sunday Kamoli said he was still in charge of the military.
“I haven't gotten any formal letter from anybody and that is to say that I am still the commander of the Lesotho Defence Force,” Kamoli told Reuters.
(READ MORE: Lesotho faces brain drain)
Lesotho, a mountainous state of two million people encircled by South Africa, has undergone a number of military coups since independence from Britain in 1966. At least 58 locals and eight South African soldiers died during a political stand-off and subsequent fighting in 1998.
Besides textile exports and a slice of regional customs receipts, Lesotho’s other big earner is hydropower. The power is exported to South Africa from the massive mountain ranges that have made it a favourite of trivia fans as “the world’s highest country” - its lowest point is 1,380 metres (4,528 feet) above sea level.