A sample count of ballots today showed a clear enough trend for Muscat, 43, to make an early declaration of victory.
Projections suggested Labour had won 55 per cent of the vote on a 92-per cent turnout, which will translate into a majority of up to nine seats in the 71-seat one chamber parliament.
"It is clear that the people have chosen to stay the course," he said, urging Maltese to unite after a divisive campaign as Labour supporters took to the streets in celebration.
The victory means there will be no major disruption to the business of the European Union, whose rotating presidency Malta holds until the end of this month.
It was the first time since Malta became independent from Britain in 1964 that Labour, now located in the mainstream of European social democracy, has won back-to-back elections.
Muscat, who has been premier since 2013, went to the polls a year early after his wife was implicated in one of a series of alleged corruption cases.
Muscat denies any wrongdoing and has promised to quit if any evidence emerges of his family having secret accounts used to bank kickbacks -- as had been alleged by a high-profile blogger with a record of correctly highlighting previous scandals in the island nation.
Muscat had also come under fire for not sacking his chief of staff Keith Schembri and government minister Konrad Mizzi after they admitted having previously undeclared companies set up for them by Mossack Fonseca.
Busuttil had framed the vote as a choice between change and allowing Malta's international reputation, and its prosperity, to be shredded as a result of the taint of corruption damaging investment.
A former academic, Busuttil may now face a challenge for the leadership of his party with the preliminary count suggesting Muscat's was nearly as commanding as it was when he swept to power in 2013.
Since then, the former journalist has presided over an investment-led boom that has seen Malta's growth accelerate to three times the eurozone average and pushed government finances into a surplus.
In his second term, Muscat has promised to leverage the country's healthy finances to fund the biggest infrastructure project in its history, a 700-million-euro scheme to resurface every road in the densely-populated island nation.
He is also promising tax cuts and pension increases for working and middle class voters.
His election win will not however make the corruption issue go away with magistrates still looking into whether kickbacks were paid to members of his inner circle in relation to an investment-based citizenship scheme, a gas supply deal with China and the granting of bank licences.
Germany in particular is demanding clarification of the status of nearly 2,000 Malta-registered companies it suspects were established as vehicles for illegal tax avoidance by major German corporations.
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