Muscat went to the polls a year early after his wife was implicated in one of a series of alleged corruption cases arising from the Panama Papers data leak.
His country, the smallest in the European Union, currently holds the six-month rotating presidency of the 28- nation bloc.
"If there is a shred of truth I will immediately resign," Muscat told the European Parliament in Strasbourg, France.
Muscat said the graft claim was "a totally outright lie that has been directed towards my wife's family."
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Muscat, a 43-year-old former journalist who has been premier since 2013, is the leader of the Labour party which is expected to have a nine-seat majority in Malta's 69-seat parliament.
Official results show that Labour won more than 55 percent of the votes, beating the Nationalist Party by over 35,000 votes, a result similar to that achieved four years ago.
A judicial inquiry is under way in Malta to determine whether an offshore company disclosed in the Panama Papers leak actually belongs to his wife, Michelle. They have both denied the claims.
The leaked documents also revealed hidden offshore companies allegedly owned by the country's energy minister, Konrad Mizzi, and by Muscat's chief of staff, Keith Schembri.