Her husband, Prince William, will instead take her place, Kensington Palace confirmed here today.
"The decision not to travel was taken by the Duke and Duchess of Cambridge on the advice of the duchess' doctors," a statement said.
"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," it added.
The Malta visit, where she was to represent Queen Elizabeth II, was being seen as a royal landmark for her.
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However, Kate has been advised complete rest and is believed to be recuperating at the home of her parents, Michael and Carole Middleton, in Bucklebury, about 88 kilometres west of London.
She is suffering from hyperemesis gravidarum, the same form of severe sickness that left her hospitalised when she was pregnant with Prince George.
The 32-year-old is expecting her second baby early next year but the due date is yet to be announced.