The office of the military ombudsman said that it was investigating at least 52 cases from the public as well as serving and former members of the SANDF during the lockdown.
Many of the complaints relate to heavy-handedness, what some feel is undignified treatment and unlawful confiscation of property.
Last week, the High Court in Pretoria ordered that all officers involved in the killing of Alexandra resident Collins Khosa be suspended pending an investigation into his murder.
Khosa died allegedly after being beaten by law enforcement officers during a lockdown operation in the township.
The office said that it had already started assessing the complaints lodged from the onset of lockdown, with some already allocated for investigation.