At an inauguration ceremony boycotted by opposition parties, Pakalitha Mosisili pledged to fight HIV/Aids, the food shortage and massive unemployment.
His ruling Lesotho Congress for Democracy (LCD) won 77 out of 80 contested seats in the 120-seat parliament, and the Basotho National Party (BNP) secured 21 seats in a parallel proportional representation vote, the largest number obtained by any opposition party.
Lesotho has been politically unstable since the 1998 elections, protested by the BNP, and which culminated in an army mutiny quashed by troops from South Africa and Botswana.
'Daunting task'
When he was sworn in for his second five-year term, Mr Mosisili said that he was prepared for the challenge ahead.
"This government faces a daunting task, but we are optimistic that we will pull through," he said.
But the opposition is still not satisfied that his government is legitimate.
"This is an illegal ceremony," Justin Lekhanya, the leader of the BNP, told Reuters news agency.
"We still insist that, pending the finalisation of our forensic tests, we are still not in a position to say that the elections were free and fair," he said in reference to a recount of votes.
A new electoral system was introduced for these elections, which was intended to make it easier for smaller parties to be represented in parliament.
Before this year's poll all the parties signed an electoral code of conduct committing themselves to respect the results.
Although foreign observers declared the poll free and fair, the BNP demanded a recount.
Despite their protests, opposition parties said last Friday that they would take up their seats in parliament, which is due to open officially later this week.