"I am acting prime minister," the minister said from Maseru, citing "cabinet protocol" for his appointment while the prime minister and deputy prime minister are in South Africa.
Phooko is a member of the Lesotho Congress for Democracy party -- which forms an acrimonious coalition government with Prime Minister Tom Thabane.
The party has denied any role in the alleged coup.
Phooko's comments are the first indication that a destabilising power vacuum seen since military action early Saturday is being filled.
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Before dawn on Saturday the military attacked key police installations, and surrounded the premier's residence in pre-dawn raids.
Prime Minister Thabane fled to South Africa shortly before, after being tipped off that the military was about to move against him.
The military have since returned to barracks, denying they planned a coup and claiming no political motive.
Phooko said he would issue a statement to the nation later today, describing the political situation as "fluid".