South Africa issues arrest warrant for Prophet Bushiri
On Saturday he told his social media followers that he had left South Africa because he had received death threats.
The preacher, who was on bail and awaiting trial for money laundering and fraud, had previously said he wanted to clear his name.
It is not clear how or when Mr Bushiri left South Africa.
In an interview with the BBC, Mr Bushiri refused to reveal how he escaped.
But the BBC's Nomsa Maseko in Malawi's capital, Lilongwe, reports that one possibility being considered is that he and his wife Mary were smuggled out by a sophisticated syndicate which specialises in taking stolen cars from South Africa to Malawi.
There have also been suggestions in the South African press that he was smuggled out in Malawi's presidential jet - something which has been denied by the authorities in both countries.
How has Shepherd Bushiri caused a diplomatic row?
This has been denied by officials in both Malawi and South Africa, but a diplomatic row is brewing.
Malawi's foreign minister told the BBC that he thought the South African authorities suspected the Malawians were trying to smuggle out the controversial preacher.
"When we were coming to Malawi leaving South Africa, we were exposed to stringent checks. It is just now that we are beginning to realise that maybe there was a suspicion that we were trying to smuggle Bushiri out of South Africa," Malawi's foreign minister Eisenhower Mkaka told the BBC's Nomsa Maseko on Saturday.
On Monday morning he then complained, very publicly, on Twitter about the seven-hour delay to the president's journey, which included "vague security reasons" for thorough checks of the presidential plane.
He noted that the South African authorities had categorically stated that Mr Bushiri had not escaped on the presidential plane.
But he described South Africa's treatment of President Chakwera as "improper".
Statement on the delay of His Excellency Dr Lazarus McCarthy Chakwera, President of the Republic of Malawis' departure from the Republic of South Africa @MalawiGovt @GovernmentZA @nomsa_maseko @CyrilRamaphosa @PresidencyZA @LAZARUSCHAKWERA @EisenhowerMkaka pic.twitter.com/oqhRJ3uBlD— Min.Foreign Affairs (@ForeignMalawi) November 16, 2020