An investigation is underway by Phoenix Police, as controversy mounts over the incident. "It is my hope that justice will be served".
In a statement, officials said Phoenix Police served a search warrant on Tuesday to obtain DNA from male Hacienda Healthcare staffers.
Bill Timmons' resignation, which was unanimously accepted by Hacienda's board of directors, came as new allegations of past abuses emerged.
CBS affiliate Arizona's Family also spoke to a former Hacienda Skilled Nursing Facility manager on Tuesday, who claimed that the company's former CEO covered up another sexually inappropriate incident.
There is also "increased monitoring of the patient care areas, and increased security measures with respect to visitors at the facility". the health department said.
According to the company's website, Timmons was the CEO of Hacienda HealthCare for 28 years.
Tribal officials confirmed the woman was still in a coma when she gave birth.
The Phoenix Police Department declined a request to comment.
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Calling her case an "absolutely horrifying situation", Hacienda HealthCare board member Gary Orman said in a statement that the "unprecedented case. has devastated everyone involved, from the victim and her family to Hacienda staff at every level of our organization".
A lawyer for the woman's family released a statement Tuesday saying the family was outraged at the "neglect of their daughter" and they asked for privacy. The sources told the local TV station that the woman had a "bump" and they are trying to determine whether anyone at the facility knew about the pregnancy and either didn't report it or actively covered it up.
"We will do everything in our power to ensure the safety of every single one of our patients and our employees", Orman said.
Govenor Doug Ducey's office has called the situation "deeply troubling".
On its website, Hacienda describes itself as "Arizona's leading provider of specialized health care services for medically fragile and chronically ill infants, children, teens, and young adults as well as those with intellectual and developmental disabilities".
She demands 24-hour care, indicating that numerous facility's staff would have access to her room, as she is incapable of any communication or voluntary movement.
Sources also told ABC 15 in another report that investigators are looking into whether the patient suffered multiple sexual assaults, "including assaults on different parts of the body". In 2013, a male employee was found to have made sexually explicit remarks to patients, though no physical or sexual abuse allegations were made and the employee was sacked.
Meanwhile, a state lawmaker is considering legislation to protect patients living at long-term healthcare facilities from abuse.