South Africa's deputy president has held secret talks with a renegade Lesotho military commander, a defence official told AFP on Thursday, as an offer of partial amnesty is floated in the hope of ending a destabilising post-coup standoff.

After inking an agreement to secure snap elections in the tiny landlocked kingdom, southern African mediators led by Cyril Ramaphosa are trying to finalise a deal to end a crisis that has left the armed forces with no clear commander.

The talks may lead to partial amnesty for the man accused of leading the August 30 putsch, a senior official in Lesotho's defence ministry said.

Lieutenant General Tlali Kamoli is suspected of leading the early morning raid on Prime Minister Tom Thabane's residence and the national police headquarters, which killed one police officer and injured nine.

He has since refused an order to relinquish command and has armed a small group of loyal fighters.

Lesotho police are investigating him for two crimes linked to the August 30 assault: high treason and murder.

Thato Mohasoa, political secretary for the Lesotho defence ministry, told AFP that the government was "amenable to making reasonable compromises" to end the logjam.

Mohasoa said the South African leader quietly met with Kamoli last week as well as with the newly appointed military commander, Maaparankoe Mahao, and the Lesotho police commissioner, Khothatso Tsooana.

Mohasoa and colleagues have made security recommendations to Ramaphosa, during his fifth visit to Lesotho as mediator for regional bloc SADC.

- Amnesty a sensitive issue -

Mohasoa said authorities would be willing to provide the suspected coup leader his full retirement package "though we aren't obliged to for a dismissed official."

But more sensitive is the amnesty -- perhaps for high treason, but not for murder.

"We can discuss possible amnesty for politically motivated reasons," he said. "But not for what's considered purely criminal actions."

Whether Kamoli will accept the offer - which may include prosecution and perhaps jail-time - "That's the million-dollar question," said Mohasoa.

The military spokesman, Major Ntlele Ntoi, could not be reached for comment.

Kamoli aside, Ramaphosa will also have to try to re-build trust between the country's two most important security services - the Lesotho Defence Force and Lesotho Mounted Police Service.

In just the latest in a series of clashes on September 30, a night-time shootout between soldiers and police on the outskirts of the capital Maseru left two more officers shot and wounded.

A top Lesotho police official told AFP he saw no major obstacle to rebuilding ties with the military if the coup leader and his allies, who have stymied criminal probes into transgressions by troops, are removed.

"We still have good cooperation with some members of the army; the problem is with just a small group of soldiers involved with these cases," said Moshe Raleting, the Senior Assistant Commissioner of Police.

"For that, we're solely depending on Mr. Ramaphosa to help deal with this."

Ramaphosa, mediating on behalf of the Southern African Development Community, has already reached a deal that allowed the re-opening of parliament - which had been shuttered for four months.

As part of the agreement elections have been moved up two years to February 2015.