Opening the proceedings in the Pretoria High Court he said evidence that might jeopardise criminal investigations would not be exposed.
"Witnesses who might be called during the public phase who might also have been approached in the criminal investigation will not be questioned with regard these aspects of the investigation in public.
Baqwa emphasised that the public hearings were complimentary to the investigation into the allegations of corruption in the arms procurement programme.
Three government agencies - Baqwa's office, the National Directorate of Public Prosecutions and the Auditor-General's Office -- are probing between 40 and 50 allegations of wrongdoing in the arms deal at the request of Parliament's watchdog public accounts committee, Scopa.
In terms of the arms procurement package, South Africa will over the next few years acquire four corvettes and three submarines, 30 light utility helicopters, 24 Hawk lead-in fighter trainers and 28 Gripen advanced light fighter aircraft.
A team of about 30 members from the three agencies and a number of experts contracted from outside are handling the criminal and forensic probe.
The hearings are scheduled to continue for two months.
Baqwa said the hearings would allow the public to be informed of what the arms deal saga was all about.
The hearings would also not be of accusatorial nature.
"This is another phase in the process," he said.
Baqwa is chairman of the panel leading the hearing.
The other two members of the panel are Herman van Zyl of the Auditor-General's office and Silas Ramaite of the National Directorate of Public Prosecutions.
Baqwa said allegations levelled against the programme included improper conduct and maladministration.
It was in the public interest that all aspects of the arms deal be investigated.
"Our intention is to proceed with speed."
Baqwa briefly allowed television cameras into the courtroom to film footage of the venue.
He said an application would be heard later on whether to allow broadcasters to record and televise proceedings.- Sapa