Speculation was mounting on Saturday that Lesotho's Prime Minister Thomas Thabane could step down earlier than expected after he failed to show up in court to face charges of murdering his estranged wife.

Thabane is accused of having acted in "common purpose" in the June 2017 killing of 58-year-old Lipolelo Thabane, whom he was in the process of divorcing.

Thabane, now 80, had been due in court on Friday for a preliminary appearance where he was expected to be formally charged.

But he travelled instead to neighbouring South Africa for what his office said was "emergency" medical attention. He is expected to return on February 27 to resume his case after his lawyers said he had a sick note.

"While we admit that is quite coincidental, we shall have our own means to ascertain this state of affairs," Mokete told AFP.

He said no arrest warrant has been issued as yet and that "new arrangements" would be made for Thabane once he was "fit for an appearance".

Thabane announced this week he would step down on July 31, bowing to pressure from members of his All Basotho Convention (ABC) party, who accused him of hampering investigations into the killing.

But party officials said he could leave office even earlier.

"If all arrangements are in place before July he is ready to go, even tomorrow," ABC secretary general Lebohang Hlaele told AFP, adding that parliament would be meeting next week to work on the "finishing touches".

"Anything is possible now as he might just wake up the next morning to announce his departure," said Hlaele, who is also the prime minister's son-in-law.

The accusations against the prime minister came after communications records from the scene of the murder included Thabane's mobile phone number.

His current wife Maesaiah Thabane, 42, whom he married two months after Lipolelo's death, is considered a co-conspirator and has already been charged with murder.

Lesotho prime Minister Thomas Thabane and his wife Maesaiah Thabane attend Thabane's inauguration in Maseru. (Samson Motikoe, AFP)

Thabane is no stranger to political unrest. He suffered a failed coup attempt two years after he was first named prime minister in 2012, and fled to South Africa.

After two years in exile, he returned to Lesotho in 2017 and won snap elections.

In his inaugural speech, Thabane described his wife's murder as a "senseless killing". He and Maesaiah - who at the time had the status of a "customary wife" - both attended Lipolelo's funeral.

Hlaele said Thabane had the "right to stand before courts".

"I don't believe that he would kill anyone," Hlaele told AFP. "But that's not for me to say."