The aircraft carrying Chilima, 51, left the capital Lilongwe at 09:17 a.m. (0717 GMT) on Monday but was unable to land at Mzuzu airport as scheduled at 10:02 a.m. due to poor visibility.
It was ordered to return to the capital but went off the radar and aviation authorities could not make contact with it.
"I'm deeply saddened, I'm sorry to inform you all that it has turn out to be a terrible tragedy. The search and rescue team has found the aircraft near a hill... they have found it completely destroyed with no survivors," Chakwera, said.
Chakwera said in an address to the nation that the crash site was in a mountainous part of the Chikangawa Forest.
Chilima, seen as a potential candidate in next year's presidential election, was arrested in 2022 over graft allegations.
However, a Malawi court dropped the charges against him last month after the director of public prosecutions filed a notice for the case to be discontinued. Chilima has denied wrongdoing.
(Reporting by Frank Phiri in Blantyre; Writing by Tannur Anders and Alexander Winning; Editing by Bate Felix)

Saulos Klaus Chilima, Malawi deputy president during the 5th Global Conference on the Elimination of Child Labour at Durban International Convention Centre on May 15, 2022 in Durban, South Africa. During the week of 15 to 20 May 2022, the Government of South Africa will host the 5th Global Conference on the Elimination of Child Labour to share good practice and to push for accelerated action.(Photo by Gallo Images/Darren Stewart)
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