This was after an apparent coup in Lesotho over the weekend, a government spokesman said.
Thabane fled the small mountain kingdom for South Africa early on Saturday, hours before the army surrounded his residence and overran police stations in the capital Maseru, in what the prime minister called a coup by the military.
(READ MORE: Lesotho's deputy premier in charge after PM flees “coup”)
Lesotho's army denied seeking to oust Thabane, saying it moved against police suspected of planning to arm a political faction in the southern African nation. One policeman was shot dead and four others wounded.
The unrest stems from a power struggle between Thabane, who is supported by the police, and Deputy Prime Minister Mothetjoa Metsing, who has the loyalty of the army, diplomats said.
Tension had risen since Thabane suspended parliament in June amid feuding in the two-year-old governing coalition.
(READ MORE: Gunfire heard in Lesotho, diplomats report apparent coup attempt )
In Maseru, the atmosphere was quiet but tense on Monday after the police commissioner said soldiers had carried out further raids on police installations and even officers' homes, taking away weapons and uniforms.
Commissioner Khothatso Ts'ooana told Public Choice FM radio station that this meant police would not be able to carry out their normal duties. Police stations were deserted and some officers had fled over the border into South Africa.
The Southern African Development Community (SADC) defence and security troika, which includes officials from South Africa, Namibia and Zimbabwe, met Thabane through the night to try to find a peaceful settlement to the crisis.
Talks were due to resume on Monday but it was not clear if Metsing, who Thabane says orchestrated the coup, would be in Pretoria to take part.
"President Zuma will meet the Lesotho prime minister this morning. It is part of the decision taken by the SADC troika on Sunday," said Nelson Kgwete, a spokesman for South Africa's Department for International Relations and Cooperation (DIRCO).
"It was resolved that all parties should be consulted to find a peaceful solution," Kgwete added.
Thabane told Reuters on Saturday he had fired the 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.
Lesotho, a mountainous state of two million people encircled by South Africa, has suffered a several 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, when Pretoria sent in troops.
Besides textile exports and a slice of regional customs receipts, Lesotho's other big earner is hydropower and water, both of which it supplies to neighbour South Africa.
(WATCH VIDEO: Lesotho Highlands Water Project)
Lesotho's 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.