South Africa will not tolerate a military coup in Lesotho, international relations and cooperation minister Maite Nkoana-Mashabane has warned.

Nkoana-Mashabane briefed journalists at Luthuli House on Sunday about the African National Congress’s (ANC's) international relations discussion document ahead of the party’s policy conference at the end of June.

She was asked whether there was concern in South Africa about the military in Lesotho not accepting the result of the election last week, after former prime minister Pakalitha Mosisili lost.

"Not in any corner of our [Southern African Development Community], not in any corner of our continent will we ever tolerate a military coup," she said.

"This was made very, very clear to everyone in Lesotho two weeks ago. They have just had an election a year and a half ago, and they have also undertaken to go back to the reforms [on the role of the police and the military, which have been supporting leaders from opposing parties] which they themselves say has bedevilled focus on governance," she said.

"So the coup thing, I think it is as clear as [daylight], we will not allow it to happen, not in our backyard. That’s not a threat; it's just the way it is."

Nkoana-Mashabane has, however, said as far as she knew, there was an ongoing process of setting up the government.

"The results have been announced. We haven’t officially been informed of any other thing that is otherwise," she said.

"So we take it that Lesotho's election has gone ahead and that there will be that acceptance. Of course, we will continue to monitor and support the Basotho in their endeavour to find peace," she said.

Mosisili's rival Tom Thabane, who was prime minister before Mosisili stepped up after elections 18 months ago, is expected to take office soon after his All Basotho Convention party won 48 out of the 120 parliamentary seats in the June 3 election. South Africa has provided support to Lesotho in the run-up to the election, with Deputy President Cyril Ramaphosa tasked with facilitating a peaceful outcome there on behalf of SADC.