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.