Both the injured men were soldiers who had tipped off Thabane about the planned August 2014 coup when the military attacked several police installations and the prime minister's residence, killing one police officer, the adviser said.
"The two guards went against their own men that day, absolutely," said the official, speaking on condition of anonymity, suggesting that yesterday's assault could be linked to the failed coup.
The bodyguards were not accompanying the prime minister at the time.
"We're still trying to figure out the motives. My gut-feeling is that what's happening now is to frustrate the election process," the adviser added.
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Lesotho's February 28 elections are being held more than two years early in order to restore stability following the August 30 coup attempt.
On the morning of the attempt, Thabane, 75, was tipped off about the plan and fled to safety across the nearby border into neighbouring South Africa before his official residence was raised by soldiers.
Though tensions have eased, police say they are still investigating recent claims that foreign "mercenaries" entered Lesotho to assassinate Thabane and other leaders.
The army, however, is still seen by many as being behind the August putsch.
In October 2014, South Africa's deputy president Cyril Ramaphosa helped broker a political agreement that re-opened parliament for the first time since June and pushed the polls forward.