Twenty-eight female guards were unfairly dismissed by a security company because the client‚ Metrora.
The army will not rest until it had exhausted all the options before accepting HIV-positive recruits.
This comes after a Pretoria high court ruling that it was unconstitutional for the army to discriminate against recruits with HIV-Aids.
Addressing the media on Friday, the chief of the South African Army, Lieutenant-General Solly Shoke said he was concerned about the implications the ruling might hold for the profile of the army.
Shoke blamed the ruling for focusing more on HIV.
"It is unfortunate that this ruling does not consider the broader picture," he said. "The army has a comprehensive health assessment, which implies we check everything.
"As a soldier you can be expected to run 20km at any time. If you have heart problems you might collapse and die."
He said it was international practice for any company to measure people against a specific job profile, which stipulates the qualities individuals should have for a specific post. In the force the criteria required one to be fit.
Shoke said he would discuss the next step with the surgeon-general. They would seek legal advice to ensure they fulfilled their obligation to all parties.
He said the army managed soldiers infected by HIV while working and that the outcome of the discussions would affect the 2009 intake of soldiers.
Sikhumbuzo Maphumulo, the attorney representing the complainants, said they were ready to challenge any legal action brought by the army.