In a statement from the Ministry of Foreign Affairs, Dr Chakwera said he has learnt "with deep sense of shock and profound sadness" on the passing of the Duke.
"Prince Phillip inspired the lives of countless young people and earned affection of generations across the Commonwealth and around the world," he added.
Prince Phillip died at Windsor Castle, in the United Kingdom at the age of 99.
He has been married to the Queen for 72 years.
He has since been accorded a 41 gun salute.