"The public will be updated of any developments on the situation as facts are established,"
Saulos Chilima was on board when the aircraft "went off radar" on Monday morning after taking off from the capital, Lilongwe, according to the president's office.
It further said that attempts to "make contact" with the aircraft were unsuccessful and that rescue operations were still underway.
"The public will be updated of any developments on the situation as facts are established," Malawi's Office of the President and Cabinet said.
A Malawi Defence Force plane left the capital at 9.17am (8.17am UK time), secretary to the president Colleen Zamba said in a statement.
The aircraft had been scheduled to land at Mzuzu International Airport at 10.02am, a trip covering a distance of about 370km.
Local media reports Mr Chilima, 51, had been on his way to the funeral of Ralph Kasambara, a lawyer and former minister.
Malawian President Lazarus Chakwera has cancelled a trip to the Bahamas and ordered authorities to "conduct an immediate search and rescue operation to locate the whereabouts of the aircraft".
Mr Chilima had been arrested in 2022 after Malawi's corruption watchdog alleged he was rewarded for helping two companies get government contracts.
He denied any wrongdoing and last month the charges were dropped, with no reason given.