Nyuse promises to modernise the economy and maintain peace in the east African state.
Opposition leader Afonso Dhlakama, whose Renamo party says last year's vote was fraudulent, boycotted the ceremony. Earlier this month, the former civil war rebel chief threatened to split the country in two because of the election row.
(READ MORE: Renamo leader to challenge Mozambique vote, but vows "no more)
Renamo fought a 16-year civil war against Nyusi's Frelimo movement before signing a peace deal in 1992, with the former Portuguese colony now looking to escape years of poverty by tapping into its huge energy resources.
"Mozambicans will never, ever fear the menace of arms," Nyusi said on Thursday, alluding to tensions between the Frelimo and Renamo groups. "I assume the presidency willing and available listen to all parties and the people."
Mozambique sits on large coal fields and has off-shore energy reserves. But it is among the world's least developed nations, with the majority of its more than 25 million people living in poverty.
Nyusi, 56, said he would ensure exploration and industrial activities were conducted in a "responsible and transparent manner, contributing to the expansion, transformation and modernisation of the economy".
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Frelimo is a former Marxist liberation movement that has ruled Mozambique since independence in 1975. Opposition groups say its tight grip on power has left many ordinary Mozambicans excluded from economic and social progress.
Renamo members of parliament refused to take up their seats this week to protest against last year's vote, and Dhlakama pointedly spent the day on Thursday visiting people hit by recent severe floods that have left thousands homeless.
Nyusi is a former defence minister. The previous president, Armando Guebuza, was also a member of Frelimo and was barred by the constitution from standing for a third term.