“An unusual, perfect storm of human error” by child welfare workers preceded the death of a 6-year-old boy whose family had been the focus of multiple abuse investigations, a top de Blasio administration deputy testified Wednesday.

“The city failed” the boy, Zymere Perkins, as did the Administration for Children’s Services, the city’s child-welfare agency, Dr. Herminia Palacio, the deputy mayor for health and human services, told a New York City Council oversight committee.

“Those involved in the Zymere Perkins case markedly failed in their duties,” Palacio said in testimony before the council’s Committee on General Welfare.

Zymere died in September after being brought to a hospital with bruises and a head injury. The boy’s mother and her boyfriend face charges in connection with his maltreatment.

On Monday, Palacio’s subordinate overseeing the agency, Gladys Carrión, abruptly resigned, a day before separate reports from the state and city criticized how her agency broke procedure while investigating allegations the boy was abused and neglected.

Front-line workers and their supervisors failed to do due diligence, contact physicians or family members who could shed light on the boy’s abusive, dysfunctional family, or take other basic best-practice steps, according to the reports.

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Carrión, who broke down during an October council hearing into the agency’s failings, did not attend Wednesday’s hearing.

Councilman Stephen Levin (D-Brooklyn), the committee chairman, lamented that agency workers — nine of whom have been disciplined or fired — did not “connect the dots.”

“These harrowing reports show that throughout his short life, Zymere Perkins was essentially tortured,” Levin said. “We all bear a responsibility as a city for his death.”

The state this month ordered the city to hire an independent overseer to scrutinize the agency’s practices.

Public Advocate Letitia James, noting that many of the recent killings of children involved mothers’ boyfriends, urged the administration to field an ad campaign targeted to such families, perhaps featuring singer Beyoncé, to discourage allowing a child to be cared for by someone who is unqualified.

“We’ve done a poor job at saving babies,” James said.

Palacio declined to discuss details of recent cases, including that of Jaden Jordan, 3, who died after being found unconscious and covered in excrement in his Brooklyn home. Workers got a report of abuse against Jaden but reportedly went to the wrong address.

Each year, the agency investigates about 55,000 cases involving 80,000 children, and places about 3,000 or 4,000 children into foster care.