Terry Thornton, spokeswoman for the California Department of Corrections and Rehabilitation, told ABCNews.com that Atkins had been placed in the prison hospital's hospice a few days ago when death seemed "imminent."
She received round the clock pastoral care, a service provided to inmates at that hospital so they don't die alone.
"It's just an effort to bring some dignity to inmates in the last time they have on Earth," Thornton said.
Atkins, 61, was diagnosed with brain cancer last year. The disease spread and Atkins, whose left leg was subsequently amputated, was paralyzed over most of her body by the time she died.
She was wheeled into the parole hearing on a gurney Sept. 2, her head covered in a pink and purple knitted cap. The cross she once carved into her forehead as a sign of loyalty to Manson was no longer visible.
Her face bloated, Atkins slept through most of the hearing, but spoke a few words of the Bible's Psalm 23, chiming in when cued by her husband and attorney James Whitehouse.
Atkins' family had pleaded with the parole board to show her mercy and let her die at home. But hearing officials cited the "atrocious" and "dispassionate" nature of the murders committed in 1969.
Atkins was one of five people convicted of the murders of pregnant actress Sharon Tate and six others in a two-night murder spree ordered by cult-leader Manson.
Atkins, Manson, Leslie Van Houten, Patricia Krenwinkel and Charles "Tex" Watson were sentenced to death. Their sentences were later commuted to life in prison after California temporarily abolished the death penalty in 1972.
Atkins was the longest-serving female inmate in the state of California at the time of her death. In another three days, that title will be passed on to Krenwinkel who was booked into the system shortly after her co-defendant.
Atkins' body was released to the coroner's office which will make arrangements with the family.
Family members of their victims, including Tate's sister and the nephew of hair stylist Jay Sebring, attended Atkins' parole hearing to ask that she remain behind bars until her death.
The family members of her victims still had harsh words for Atkins, reminding the panel that she was a cold-blooded killer who had not once apologized to any of them for the lives she took in such a brutal, gruesome fashion.
"There has never been any hate in my for these people," said Debra Tate, a sister of murdered actress Sharon Tate, said while imploring the panel to deny Atkins' parole. "I am incapable of hating."
Tate noted that in denying her family an apology and seeking parole, Atkins has denied the Tate family a chance at freedom from her crimes.
Since her conviction, Atkins has been denied parole 12 times.
The two other female Manson murderers, van Houten and Krenwinkel, are up for parole next year.
She is the longest-serving female inmate currently incarcerated in California, entering the system on April 23, 1971 -- five days before Krenwinkel.
Family members of her victims pleaded with California officials to keep the one-time Manson acolyte follower behind bars.
Debra Tate and Anthony DiMaria, a nephew of hairstylist Jay Sebring, were among those who testified at the hearing at the Central California Women's Facility, according to Sandi Gibbons of the Los Angeles County District Attorney's Office.
Manson is next up for parole in May 2012. Watson is up in November 2011.
Atkins hardly looks the part of the cold-blooded murderer, but she has been described as one of the more vicious of the "Manson women."
If parole had been granted, it would have been an act of mercy that she so notoriously denied her most famous victim – an 8-months pregnant actress Sharon Tate, who was murdered in her Los Angeles home on Aug. 9, 1969 alongside Jay Sebring, Abigail Folger and Wojciech Frykowski. Teenager Steven Parent was also murdered that night in Tate's driveway for simply being in the wrong place at the wrong time.
In one of the most chilling moments of the Manson Family's crime spree was Atkins' account of how the actress pleaded for mercy for her unborn child.
"She asked me to let her baby live," Atkins said at a parole hearing 16 years ago. "I told her I didn't have mercy for her."
Cult-leader Manson, buddy Charles "Tex" Watson and two of his infamous "Manson women" -- Patricia Krenwinkel and Atkins -- were sentenced to death for the Tate murders and the slaying of grocery store executive Leno LaBianca and his wife Rosemary on Aug. 10, 1969. A third woman, Leslie van Houten, was convicted along with the others and sentenced to death on two counts of murder for her role in the LaBianca murders.
Anthony DiMaria, nephew of Jay Sebring, a hairstylist to the stars who died as he tried to protect Tate and her unborn child, said he will once again make the trek from Las Vegas to California in hopes of keeping his uncle's murderers out of society.
"She's more than a Manson follower," he said of Atkins. "She's a mass murderer."
Paroling Atkins because she was dying of cancer -- a disease he called "fate" -- would send the wrong message, especially given Manson's dark following as some kind of anti-hero, DiMaria told ABCNews.com.
"Like it or not she and these crimes have had a huge impact, obviously on our family but also culturally," he said.
Atkins had spent most of the last 38 years at the California Institution for Women in Corona, Calif., the same facility that houses Krenwinkel and van Houten. She was moved to Chowchilla last year after being hospitalized.
Thornton said Atkins has been an active inmate with a "well-documented record" of volunteerism and participation in events and groups dealing with personal growth, religion, substance abuse, self-help and fundraising.
She's also earned over the years "above average to excellent work performance ratings," Thornton said, and has held a variety of jobs working in laundry, maintenance and the yard crew as well as positions as a teacher's aide, a clerk and a porter.
Thornton said Atkins also logged five rules violations in her 38 years in prison, the most recent in March of 1993. She did not have specifics about the violations.
She's also been married twice while behind bars. Her second husband, James Whitehouse, has become her most vocal supporter.
Former Los Angeles prosecutor turned author Vincent Bugliosi -- who put Manson and his followers behind bars and penned "Helter Skelter," the best-selling account of the crimes -- told ABCNews.com last month that Atkins was the only one of the group that he might accept parole for.
Bugliosi said he was not an advocate for her release, but believes that Atkins' freedom would have meant little opportunity for her besides death outside a prison.
"They were all sentenced to death, and that would have been the proper punishment," he said of the Manson murderers. "All of them, except Susan Atkins ... should spend the rest of their lives behind bars. They should be very happy their lives were spared and not take it to the next level."