A top Lesotho defence official has urged regional powers to "remove" an influential military commander for flouting a peace deal meant to stabilise the tiny African country two months after an attempted coup.

The defence ministry's principal secretary accused Lieutenant General Tlali Kamoli of harassing rivals and marshalling forces, despite an agreement to relinquish his command.

Echoing a confidential letter to South African Deputy President Cyril Ramaphosa, Thato Mohasoa told AFP on Thursday that the Southern African Development Community should "remove" Kamoli, who is accused of being behind an August 30 coup attempt.

"SADC should use any means at their disposal -- including persuasion," he said.

Kamoli is accused of ordering a pre-dawn military raid on Prime Minister Tom Thabane's residence and the national police headquarters.

Under a deal inked last month Kamoli agreed to hand over control to his deputy commander and exercise no "authority or undue influence" over the army during an indefinite "leave of absence".

In the letter, first obtained by the Lesotho Times, Kamoli is accused of holding multiple meetings with underlings, stating he was still "substantive commander" of the Lesotho Defence Forces.

During the meetings he would specify how "resources" were to be "utilised".

The letter also claims Kamoli loyalists assaulted supporters of a rival military commander.

Ramaphosa was in Lesotho again on Thursday, the politician's seventh visit to Maseru since taking over as lead SADC facilitator in the crisis in September.

Mohasoa said Ramaphosa "appreciated our concerns, that we're walking a very thin line -- and it's important to step cautiously".

Early last month, Ramaphosa helped broker a political agreement that re-opened Parliament for the first time since June and pushed national elections forward to February 2015, more than two years early.

Friction between the Lesotho military and police routinely turns violent and has been a major destabilising force in recent months.

A night-time shootout between soldiers and police on September 30 left two officers shot and wounded.

Under the October security accord, Kamoli's rival Maaparankoe Mahao and Lesotho police commissioner Khothatso Tsooana similarly hand over authority to enable their two security forces to re-establish a "harmonious relationship".