The South African man currently detained in Mozambique is "well in custody" and is "facing a number of charges", the Department of International Relations and Cooperation (Dirco) said on Sunday.
News24 previously reported that André Hanekom, 60, and two Tanzanians were arrested on December 31, and were named by Mozambican authorities as allegedly being part of a jihadist group operating in the region.
According to AFP, the group faces charges including murder and crimes against the state.
Allegedly, Hanekom was responsible for the logistics of the group and was shot while trying to resist arrest in August. Weapons were reportedly found at his home.
Dirco spokesperson Ndivhuwo Mabaya said minister Lindiwe Sisulu has received a report from South African High Commissioner to Mozambique Mandisi Mpahlwa on Hanekom.
"Minister had directed Ambassador Mpahlwa to visit Mr Hanekom after receiving concerns from the family and friends about his health. The high commissioner confirmed to the minister that Mr Hanekom is well in custody and is facing a number of charges. He will appear in court soon," said Mabaya in a statement.
He said Mpahlwa was monitoring the case, "keeping the family informed and offering consular support".
"The Minister also directed the High Commissioner to always keep the family informed of all the developments," said Mabaya.
Hanekom's daughter Andrie previously told Netwerk24 that the family believed that influential people were misusing the Mozambican police, as they wanted to get their hands on his beach property in Palma, in the northern province of Cabo Delgado.
Hanekom and his wife, Francis, have lived in the region for 26 years.