The 61-year-old South African was being held in that country over terrorism charges, according to ministry spokesperson Ndivhuwo Mabaya, and the minister has requested information following press reports that Hanekom's daughter, Amanda, had confirmed that her father had died in custody on Wednesday morning.
Mabaya said the ministry was also engaging with High Commissioner (Ambassador) Mpahlwa to ensure that the family was assisted with obtaining and repatriating the deceased’s remains home.
"Most importantly, the minister also directed the high commissioner to engage with the authorities in Mozambique around this matter, so that we understand what has happened and what led to his death. As you are aware, the gentleman was in prison," Mabaya said.
Hanekom's daughter told the press that her father had been transported from northern Mozambique to the town of Pemba ahead of his court appearance on terrorism charges, and to a meeting with the high commissioner on Friday, when he suddenly and inexplicably got ill.
"We are hoping to recover my father's remains in order to determine the cause of death," Amanda told the press.
Hanekom was detained and was facing a number of charges, the ministry said, including that of terrorism, after he was arrested on 31 December.
Mozambican authorities named him as being part of a jihadist group operating in the region of that country that borders southern Tanzania where a low level insurgency has been taking place.