Kate has been suffering from the same severe morning sickness that struck during her pregnancy with Prince George.
The Duchess of Cambridge had 10 engagements lined up for the two-day tour
Her agenda included 10 engagements in two days of celebrations for the 50th anniversary of the island nation's independence. An added complication is the weather, with temperatures of up to 30 degrees expected in the Mediterranean this weekend.
Kate was desperately keen to go as the Queen had personally asked the Duchess to represent her. Malta is very close to the monarch's heart as she and Prince Philip spent time living there in the early years of their marriage during his tour of duty as a naval officer.
Kate is thought to be eight weeks pregnant with her second child
A statement from the Palace said: "Her Royal Highness continues to suffer from the effects of Hyperemesis Gravidarum.
"The decision not to travel was taken by the Duke and Duchess on the advice of the Duchess's doctors.
"The Duke is honoured to represent Her Majesty The Queen on the visit, which commemorates the 50th anniversary of Malta's Independence. The visit itinerary remains unchanged."
Prince William will go instead of Kate
A few weeks ago, Wiliam and Kate were forced to bring forward the announcement that they were expecting their second child as the Duchess pulled out of several events. She withdrew from appearances at Oxford University and Harry's Invictus Games.
Kate, who is thought to be eight weeks pregnant, has been resting at home in Kensington Palace under the care of her medical team. Royal doctors Alan Farthing and Guy Thorpe-Beeston were both present at Prince George's birth last summer.