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William, who was stepping in for the Duchess of Cambridge, née Kate Middleton, whose acute morning sickness meant she was too ill to make the trip, was met by President Marie Louise Colerio Preca.
Amid bright Mediterranean sunshine, the 32-year-old royal arrived at San Anton Palace where he toured the grounds and planted a tree.
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Scores of people lined the streets of Valletta, the country's capital, where they greeted William and gave him gifts for his young son Prince George.
While speaking to the well-wishers William apologised that his wife couldn't make the trip she had been so keen on undertaking.
"Sorry Catherine can't be here," he reportedly told royal fans. "She's doing so-so."
Saturday 20 September
- The Duke will call on Prime Minister Joseph Muscat at the Auberge de Castille and view the In Guardia re-enactment at the Palace Square, Valletta.
- At the National Library he will view a number of historical documents, including letters from kings Henry VIII and George II, and the original citation awarding the George Cross to Malta.
- In the evening he will attend an official Independence Day reception at the Upper Barrakka.
- The Duke will stay overnight as a guest of President Marie-Louise Coleiro Preca at San Anton Palace.
Sunday 21 September
- Prince William will attend Mass at St John's Co-Cathedral and later view the two Caravaggio masterpieces.
- The Duke will visit to Centru Access in Vittoriosa for a meeting with the staff and clients of Agenzija Zghazagh.
- William will conduct a walkabout in Vittoriosa and a tour of the Church of St Lawrence followed by a boat trip in Grand Harbour.
- Finally he will attend a Garden Party hosted by the British High Commissioner