Gardai stood down a search for the 17-year-old, who had been missing since Thursday, after his remains were discovered in Bray.
Shane who had gone missing from Newbridge, Co. Kildare two days ago had last been seen in Tallaght.
Taking to Twitter, the singer expressed her anguish in a series of heart-breaking posts.
“I have now formally identified the remains of my son, Shane,” she wrote. “May God forgive the Irish State for I never will.”
She added: “Now Tusla want to discuss with me ‘a media release’ no doubt wishing to have me join in their efforts to make this death of my child seem like it wasn’t at the hands of the Irish State."
She added: “Refusals to accept responsibility. Couched as always in the omnipotent and false concern they claim to have for the privacy of the children who die on their watch.”
In another tweet, Sinead said she was "going to take private time now to grieve my son".
A spokesperson for Tusla said the body does not comment in cases where a child in care dies. She said in such circumstances, the child’s case is passed to the National Review Panel for examination.
Earlier, Sinead had paid tribute to her “beautiful son, Nevi’im Nesta Ali Shane O’Connor, the very light of my life” (who) decided to end his earthly struggle today and is now with God.
“May he rest in peace and may no one follow his example. My baby. I love you so much. Please be at peace.”
Sinead said earlier this week that her son had gone missing from Tallaght Hospital.
Shane McGowan was among those who paid tribute to tragic Shane.
The tragic teenager was named after the former Pogues frontman.
In an online post McGowan described Shane as “beautiful boy” and said he loved him.
“Sinead you have always been there for me and for so many people, in this world you have been a comfort and you have been a soul who is not afraid to feel the pain of the suffering and you have always tried to heal and to help.
“I pray and Victoria prays that you can be comforted now and find strength and healing and peace in your own sorrow and loss, he was a beautiful boy and I loved him and I pray that he can be at peace and also be able to stay connected with you."
Singer James Vincent McMorrow said he was "heartbroken" to hear about Sinead O Connor's son.
"Another life gone too soon," he tweeted. "Sinead posted this poem he wrote last year and I love it. Grief is the thing with feathers, take care of each other, send your love to Sinead. X"
Socialist Party TD Ruth Coppinger said more funding needed to be given to deal with mental health in Ireland.
“How incredibly sad and horrific for Sinead O'Connor and Donal Lunny to experience the loss of their son this way. Also, very strong to not hide the cause of death. The mental health crisis is real and disgracefully neglected: massive investment & resources needed by the state. RIP.”
Psychologist and broadcaster Emma Kenny described the news as “tragic beyond belief” and said young people are being failed in society.