Mr Thabane met with South Africa's President Jacob Zuma and security chiefs from neighbouring countries this week in an effort to end a political crisis in the mountain kingdom.
South African police had escorted him home afterwards, said Samonyane Ntsekele, an advisor to Mr Thabane.
"He's in state house. He's the one in charge. South African police are with him and he is well secured," Mr Ntsekele aid.
"He saw the king today and we hope they will work together as a team. I don't know what has been agreed."
Lesotho, a mountainous state of two million people encircled entirely by South Africa, has a parliamentary democratic government and the king serves largely a ceremonial role.
Mr Thabane fled to South Africa early on Saturday, hours before the army surrounded his residence and overran police stations in Maseru in what the prime minister called a coup.
Lesotho's army said it had not tried to oust Mr Thabane but rather moved against police suspected of planning to arm a political faction. One policeman was shot dead and four others wounded.
The unrest stems from a power struggle between Mr Thabane, who is supported by the police, and Deputy Prime Minister Mothetjoa Metsing, who has the loyalty of the army.
Tension has risen since Mr Thabane, who has accused Mr Metsing of orchestrating the coup, suspended parliament in June amid feuding in the two-year-old governing coalition.
Mr Thabane said at the weekend he had fired the army commander, Lieutenant-General Kennedy Tlali Kamoli, and appointed Brigadier Maaparankoe Mahao to replace him. But Mr Kamoli has not said publicly that he will stand down.
Lesotho has suffered several coups since independence from Britain in 1966 including one in 1998 in which dozens died.