Recording equipment was found planted under Thomas Thabane’s desk and near his office landline, just six weeks after he took office following his party’s victory in snap elections last month.
“It is true that there were bugging devices found in the prime minister’s office and as we speak investigations to establish who is behind this are ongoing,” the premier’s spokesman Thabo Thakalekoala told AFP.
It also emerged that a biometric access control scanner at the entrance of Thabane’s office was malfunctioning.
“This is a serious breach of the prime minister’s security,” said the spokesman.
But the prime minister “remains unshaken” said Thakalekoala, adding Thabane has appealed for “calm because the situation remains under control”.
Thabane took power for a second time last month after his All Basotho Convention (ABC) secured electoral victory just four months after his return from South Africa.
Prime minister from 2012, he had fled in August 2014 claiming there was an army plot to kill him.
He only returned to Lesotho after the removal of army chief Tlali Kamoli who allegedly led the putsch.
His inauguration on June 16 was marred by the murder of his estranged wife at a village near the capital on the eve of his the ceremony.
Local media reported this week that car-tracking devices were also discovered in the official vehicles used by Thabane’s current wife.
Thabane’s party failed to get an outright majority, leading it to form a coalition with three other parties.
The government is hoping to end the political uncertainty of party splits and fragile coalitions that have long dogged the mountain kingdom.
The tiny poverty-stricken country, completely surrounded by South Africa, has been plugged with political and security instabilities since the 2014 attempted coup.