Lesotho premier Thomas Thabane failed Friday to show up in court where he was due to be charged with murdering his estranged wife, prompting police to warn they could issue an arrest warrant.

His aide initially said Thabane had gone to neighbouring South Africa for "routine" health checks, but later his office issued a statement saying he was seeking "emergency" medical attention and would appear in court on his return.

The 80-year-old prime minister is accused of having acted "in common purpose" in the June 2017 killing of Lilopelo Thabane, 58, with whom he was embroiled in a bitter divorce.

She was gunned down just two days before Thabane took his oath of office.

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.

Deputy Police Commissioner Palesa Mokete said after Thabane failed to turn up in court that police had been informed he had gone for a routine checkup.

"If we are to ascertain that he is actually trying to avoid being charged we will issue a warrant of arrest for defeating the ends of justice."

Thabane's personal secretary Thabo Thakalekoala told AFP that the prime minister was not attending court because he had gone to South Africa for a "routine" medical exam.

Prime Minister Thomas Thabane and Maesaiah Thabane, pictured alongside Zambian President Edgar Lungu, right, at Thabane's inauguration, two days after the murder of the premier's estranged wife
Prime Minister Thomas Thabane and Maesaiah Thabane, pictured alongside Zambian President Edgar Lungu, right, at Thabane's inauguration, two days after the murder of the premier's estranged wife AFP / SAMSON MOTIKOE

But in a statement later the premier's office said he left in the early hours "to seek emergency medical attention".

"The office refutes allegations that the honourable PM fled the country to frustrate delivery of justice," the statement said.

It said Thabane "will appear in court immediately after returning to the country as he had indicated before that he respects the courts".

Police said Thabane's daytime guards at State House told them that when they reported for duty on Friday "he was nowhere to be found and... that he had left with his night guards".

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

"We have a very strong case against the PM and his phone is not the only evidence that we have," Mokete told reporters.

The death shook Lesotho, a landlocked mountainous nation of 2.2 million people that has a long history of political turmoil.

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" -- attended Lipolelo's funeral.

Prime Minister Thomas Thabane was scheduled to be charged with murdering his wife
Prime Minister Thomas Thabane was scheduled to be charged with murdering his wife AFP / GIANLUIGI GUERCIA

On Thursday, Thabane had announced that he would quit office by July 31 because of his age, ahead of the end of his elected term in 2022.

It has been more than a decade since a prime minister served out a full five-year term in Lesotho.

Thabane fled the country once before, when his first coalition government was marred by political bickering, which culminated in an army-led coup in August 2014.

He sought exile in South Africa after soldiers attacked police posts and surrounded his official residence.

He returned home in 2017 and successfully ran for re-election.

Analysts said Thabane was not technically a fugitive from justice and may be playing for time.

"The prime minister for now, cannot be accused of having evaded justice because there is no warrant of arrest, there were no summons served on him, it was just politically expected that he would appear in court," said Hoolo Nyane, a constitutional law professor at South Africa's University of Limpopo.

Regional powerhouse South Africa, which completely surrounds the picturesque kingdom, has been conspicuously silent over the events in Lesotho.

President Cyril Ramaphosa currently chairs the African Union and has for years been the regional SADC bloc's Lesotho mediator.

"This has been an ongoing drama, almost like a crime novel," said Liesl Louw-Vaudran, senior researcher with the Pretoria-based Institute of Security Studies.

"Now there is definitely a need for some external intervention.

"It's very messy, it's very chaotic, it's certainly unprecedented," she said.

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