The findings stopped short of faulting individual case workers overseeing the care of Myls Dodson, but they prompted Mayor Bill de Blasio to announced a list of reforms for the Administration for Children's Services.
"We lost a child in a horrible manner. ... We want to learn from this tragedy and make changes as a result," De Blasio said at a City Hall news conference.
Dobson died this month after his father was jailed again and left him in the care of his girlfriend. She was charged with assault after allegedly telling investigators she had starved him for several days and also bound, beaten and burned him.
The review looked at interactions between Dobson's family and ACS between January 2011, when it received an allegation of abuse, and last August when it closed the case.
Among the finding was that case workers missed the fact that the father, an ex-con and parolee named Okee Wade, was in jail from September 2012 to February 2013 despite visiting his home nine times during that period. Wade's girlfriend at the time - not the one in charged in the death - told them he was at work, officials said.
Though not a requirement, the ACS considers it a "good practice" to see the primary custodian in person, said Gladys Carrion, the head of ACS. But she also stressed that Myls always appeared safe and healthy before the supervision ended.
De Blasio said he was ordering a review of all cases that include court-ordered ACS supervision. New measures include requiring custodians to appear in family court and get a judge's approval before supervision ends, and expanding ACS's access law enforcement data bases to assess whether caregivers are reliable or not.
The last major investigation into the child welfare agency came in 2011, after 4-year-old Marchella Pierce was found drugged, beaten and starved in her home. A report, issued by a panel that included de Blasio in his role as public advocate, recommended changes to how the agency handled families with complex medical issues.
The agency also said it was strengthening oversight of supervisors and manager training. Fresh guidance on note-taking and documentation requirements was also issued.
The changes were supposedly build on changes already in place after the 2006 death of Nixzmary Brown, a 7-year-old who was beaten and starved by her family without intervention by her teachers and ACS workers. Her mother and stepfather are serving long sentences in her death.
Meantime, Myls Dobson's father spoke exclusively with Eyewitness News about his devastating loss.
Eyewitness News was there when Okee Wade was released from jail Thursday after pleading guilty to racketeering charges.
"A part of me blames me," he said. "But another part of me can't blame me, because I can't blame somebody's actions on myself."
It's been more than a week since his Dobson was found dead in a Midtown apartment. Police say Kryzie King tortured the boy before he died.
Wade says he's never heard of King, and that he left his son with a friend named Jane Munroe. Police say Munroe and King are the same person.
Wade had full custody of his son before he was arrested, and he's been given a three-week furlough from jail to attend Myls' funeral.
"The first tragedy is me being locked up, and I couldn't get my son," Wade said. "And I begged them to at least let me get my son, but they said they wasn't going to let me out. Then the other tragedy is my son is murdered."
The boy's body was released to his mother, even though she did not have custody at the time of his death.
Myls Dobson's funeral is scheduled for Tuesday evening at First Corinthians Baptist Church in Harlem. The Reverend Al Sharpton will deliver the eulogy.
(The Associated Press contributed to the report)