Prime Minister Thomas Thabane fled the country, saying the country's military had surrounded his official home and seized government buildings in the capital of Maseru.
The premier took his family to neighboring South Africa after saying he received an assassination threat.
Military spokesman Major Ntlele Ntoi said there was not, in fact, a coup, but that the military was responding to a threat from "political fanatics" whom police were attempting to arm.
"What happened this morning was that the command of the Lesotho Defense Force was acting after receiving several intelligence reports that amongst the police service, there are some elements who are actually planning to arm some of the political, party political youth fanatics who were on the verge of wreaking havoc," he told Voice of America.
South African government spokesman Clayson Monyela said the military's actions had the appearance at an overthrow.
"Although no one has claimed to have taken over government through the use of force, by all accounts the activities of the Lesotho defense force thus far bear the hallmarks of a coup d'etat," he said.
Lesotho military officials said soldiers returned to their barracks Sunday and there was calm in the capital.
Meanwhile, Deputy Prime Minister Mothetjoa Metsing in control of the government in Thabane's absence. Thabane said he believes he is being targeted due to his attempt to fight corruption in the country.
Tensions have been high in Lesotho since June when Thabane suspended parliament sessions due to feuding in his unity government. He said his actions have not undermined the government, despite allegations otherwise.