"The military healthcare practitioners were deployed to hospitals as determined by the Department of Health and will remain deployed as may be required," said the SANDF.
Workers affiliated with the union have been on strike for over a week with violent protests barring doctors, nurses and patients from entering the health centres, reports Xinhua news agency.
The strike started on March 6 as the employees demanded a 10-12 per cent salary increment, but the administration had only put forward an offer of less than 5 per cent.
The union on Monday vowed in a statement to intensify the strike.
"Any form of violence and intimidation is condemned in the strongest terms and will be dealt with by law enforcement agencies," the Department of Government Communication and Information System said following the union's statement.