The dispute relates to him allegedly not respecting the election of the national executive committee that was elected in February.
According to reports, he has been suspended for six years, along with former secretary-general Samonyane Ntsekele.
His position is reportedly to be occupied by Prof Nqosa Mahao, his deputy.
It was reported this week that Thabane was facing a motion of no confidence for allegedly allowing his wife to meddle in government affairs, as political in-fighting rocked his ruling party and threatened the breakdown of his coalition government.
The motion was filed in parliament this week by a member of Thabane’s own party, raising the possibility he would call snap elections in the tiny mountainous southern African kingdom.
“We hereby move a motion that this honourable house has no confidence in a government of Lesotho led by the Prime Minister Thomas Motsoahe Thabane,” read a motion filed by ABC’s Motebang Koma and seconded by the main opposition Democratic Congress deputy leader, Motlalentoa Letsosa.
Parliament was adjourned on Monday with no date fixed for it to sit again.
While the motion did not outline reasons for wanting Thabane out, some party members had turned to local media to voice claims that the 80-year-old premier was ceding political power to his young wife, Maesaiah Thabane.
Even staunch supporters of Thabane, such as outspoken Thaba-Bosiu Principal Chief Khoabane Theko, have backed calls for his removal.
“He allowed his wife to usurp control of the party and government,” Theko told the Lesotho Times.
“What they must do is to call a special conference and resolve that Ntate Thabane should step down. He wants to play God with this government through his wife.” Ntate means sir in Lesotho.
The row comes two years after Thabane’s estranged wife Lipolelo, 58, was gunned down just two days before his inauguration.
He and Lipolelo were embroiled in a bitter divorce dispute.
She won a court case against Thabane during his first stint as prime minister affirming her position as Lesotho’s first lady instead of Thabane’s youngest wife. Polygamy is legal in Lesotho.
Known as Africa’s Switzerland because of its mountainous scenery, Lesotho has a long history of political instability and suffered coups in 1986 and 1991.
The ABC party has also been riven with internal conflict over the appointment of the new party deputy.
A pro-Thabane faction has fiercely defended the leader.
Defence minister Tefo Mapesela told parliament this week that Thabane intended to call fresh elections when parliament reconvened.
Thabane, whose coalition took office in 2017, was previously premier after 2012 elections but was forced to flee to South Africa — which entirely surrounds landlocked Lesotho — following an attempted coup two years later.