The attacker entered the premises under the pretence of visiting a patient and gained access to the hospital's female medical ward.
He entered the ward and allegedly raped the woman. Police say there were two other critically injured patients sleeping in separate beds in the room at the time of the rape.
According to the victim's mother the attacker raped her daughter for more than 20 minutes and fled after realising that one patient was about to raise the alarm.
She said her daughter was deeply distressed, and was still in hospital.
"It is unacceptable for a patient to be raped in a hospital or anywhere else," the mother said. "Where were the security guards and the nurses? She is not safe anymore. if I had the money I would take her somewhere else for treatment. That hospital is a disaster."
The woman said her daughter was admitted on December 8 after feeling light-headed. She was supposed to be discharged on Christmas Eve but the doctor said he wanted her to stay in hospital for further observation.
She said hospital manager Labius Lebotse summoned her to the hospital on Wednesday to apologise for the incident.
"He kept me waiting for about two hours and told me he was sorry about what had happened," she said. Lebotse confirmed the incident and apologised on behalf of the hospital. Department of Health spokesman Tebogo Lekgethwane said the hospital had one security officer each for ward 9 and 8 (female and chronic wards).
"Both security officers have been given masks as a precautionary measures to prevent infections.
"Ward 2 (gynaecology) also was given a security officer for both shifts," he said.
Police spokesman Colonel Lesego Metsi said the suspect appeared in the Mmabatho Magistrate's Court on Wednesday on a charge of rape.
He said the suspect was remanded in custody for further investigation and that the case has been postponed to February 22.