NEW YORK » Jonathan Carey did not die for lack of money.

New York state and the federal government provided $1.4 million annually per person to care for Jonathan and the other residents of the Oswald D. Heck Developmental Center, a warren of low-rise concrete and brick buildings near Albany, N.Y.

Yet on a February afternoon in 2007, Jonathan, a skinny, autistic 13-year-old, was asphyxiated, slowly crushed to death in the back seat of a van by a state employee.

O.D. Heck is one of nine large institutions in New York that house the developmentally disabled, those with cerebral palsy, autism, Down syndrome and other conditions.

These institutions receive two and a half times as much money, per resident, as the thousands of smaller group homes that care for far more of the 135,000 developmentally disabled New Yorkers receiving services.

But the institutions are hardly a model: They have tolerated physical and psychological abuse, knowingly hired unqualified workers, ignored complaints by whistle-blowers and failed to credibly investigate cases of abuse and neglect, according to a review by The of thousands of state records and court documents, along with interviews of current and former employees.

Since 2005, seven of the institutions have failed inspections by the State Health Department, which oversees the safety and living conditions of the residents, among other issues. One of these institutions was shut down altogether this year.

Dozens of people with direct experience in the system echoed a central complaint about the Office for People With Developmental Disabilities: that the agency fails to take complaints seriously or curtail abuse of its residents.

"I’ve never seen any outfit run the way this place is," said Jim Lynch, a direct-care worker in New York. "You report stuff, and then you get retaliated against. They want everything kept quiet. People that are outspoken attract the heat. I don’t know who to talk to when I see a problem. Nothing ever gets done."

Earlier this year, Gov. Andrew M. Cuomo forced the resignation of the commissioner of the Office for People With Developmental Disabilities after learning of the Times investigation, and said his administration would undertake a broad review of the state’s care of the developmentally disabled.

Indications are, however, that the agency is still struggling. Its new commissioner, Courtney Burke, is a well-regarded policy analyst but lacks management experience. She has taken over an agency with 23,000 employees; previously, she managed no more than seven. Cuomo has asked two veteran commissioners to review the agency’s practices, and Burke has taken some decisive steps, firing two top officials, and is trying to establish more independent investigations.

The institutions have survived in part because officials have argued that they need a place to house the most frail or physically unruly residents. But there is also big money at stake. New York has been adept at wringing large amounts of cash from Washington, earmarked for the institutions.

The federal and state governments now allocate more than $1.8 million annually for each of the roughly 1,300 residents remaining in the nine institutions, a number that has steadily risen from $1.4 million in 2007, when Jonathan Carey died.

That adds up to more than $2.5 billion a year, with about 60 percent coming from Washington.

But the state agency recently conceded that only about $600 million is being spent on the residents’ care — a still-generous allocation of nearly $430,000 per person — while the rest is redirected throughout the agency for use at group homes and care in other areas.

JONATHAN’S STORY

Jonathan Carey arrived at O.D. Heck on Oct. 7, 2005.

Two months later, unbeknown to Jonathan’s parents, Michael and Lisa Carey, the federal government barred the facility from accepting new residents financed by Medicaid for a year because of its chronic problems.

Direct-care workers were often high school dropouts, some with criminal convictions. One lower-level supervisor had a petty larceny conviction. Edwin Tirado, the employee eventually convicted of manslaughter in Jonathan’s death, had been convicted of selling marijuana and, as a youthful offender, for firing a shotgun in his attic.

Nadeem Mall, a trainee at O.D. Heck who pleaded guilty to criminally negligent homicide in Jonathan’s death, was fired from four different private providers of services to the developmentally disabled, lasting less than a year at all of them, before he was hired by the state.

For the Careys, the journey to O.D. Heck was a last resort. Jonathan was born in 1993, the older of their two sons. When he was 19 months old, the Careys were told that he was mentally retarded, and when he was older that he was autistic — functionally a 2-year-old, his vocabulary limited to "daddy" and the phrase "Where you goin’?"

On Oct. 29, just a couple of weeks after Jonathan was enrolled, the Careys arrived to find their son’s nose so swollen that they took him to the hospital. None of the staff members claimed to know what had happened, and they speculated that it had occurred during a dental procedure. Another time, Jonathan was taken to the hospital with a black eye and a broken nose. That time, the staff suggested that Jonathan might have fallen out of bed.

On a third occasion, Jonathan was taken to the hospital with severe bruising on both sides of his face.

"They basically told us that Jonathan had fallen out of a rocking chair and hit his head on a table, and I said, ‘Absolutely not,"’ Lisa Carey said.

The situation came to a head on Feb. 15, 2007. Tirado and Mall took Jonathan and another resident on an outing.

Mall first drove to his bank, leaving Tirado in the van with Jonathan and the other resident. While they were waiting, Jonathan got up from his seat. Tirado went to the back of the van and began to restrain Jonathan, trying to subdue him. Mall and the other resident, identified in court documents by his initials, E.C., later said that Tirado sat on Jonathan, who was face down, his legs flailing.

Tirado restrained Jonathan for about 15 minutes, continuing as the group drove to a gas station.

E.C., watching with apparent concern from the front of the van, told Tirado, "Get off of him," and "Let him breathe," according to Mall.

When they got to the gas station, Mall went inside to buy some drinks. Mall has testified that when he returned to the van, Tirado told him that Jonathan had stopped breathing.

The two men drove around for more than an hour with a suddenly silent boy in the back without checking on him or calling 911. They went to a video game store, where Tirado bought a special bag for his PlayStation, then to Tirado’s house, where they smoked and chatted with a neighbor, and eventually back to O.D. Heck.

An autopsy found the cause of death to be compressive asphyxia — basically, so much pressure was put on Jonathan’s chest that he could not get enough oxygen into his lungs.

State officials have said they took a number of steps to clean up O.D. Heck after Jonathan’s death.

Those included increasing the number of clinical staff members and direct-care workers and putting more emphasis on teaching residents skills that will help them move to small group homes, the agency said.

But Mary Maioriello, an employee at O.D. Heck until she resigned this year, said a culture of abuse continued to flourish. Maioriello was hired as a trainee last year, and witnessed several disturbing episodes. In one case, two employees played a game they called "Fetch," throwing French fries on the floor and laughing as one resident dived to get them, while another jumped out of his recliner and a third ate them off the floor.

"I just thought, oh my God, what is wrong with these people?" Maioriello said of the other employees, adding: "And then once I finally turned it in, I feel like it fell on deaf ears."

Little resulted from Maioriello’s reports to management. Maioriello went on leave and resigned in March, threatening to go to the news media before she left.

THE OFFICIAL RESPONSE

It was then that Kate Bishop, who supervises O.D. Heck and group homes, met with Maioriello.

In an emotional hourlong encounter that she secretly recorded, Maioriello challenged Bishop and Andrew Morgese, the agency’s head of internal affairs, who was also present, reminding them that she had reported that a resident was being regularly beaten with a stick. She asked why the matter had not been reported to law enforcement. "Were the police notified?" Maioriello asked, according to the tape, which was provided to The Times. "Because it was an assault. That is the law, that the police are to be notified when an individual is assaulted. Were they notified?"

"Well," Bishop said, "in the original report that you made, it didn’t appear to rise to the level of …"

"Hitting someone with a stick?" Maioriello asked.

"In the initial manner described …" Bishop responded.

"Really?" Maioriello said. "So what’s the severity that you have to make an assault?"

At one point during the exchange, Morgese suggested that it was the responsibility of Maioriello, a trainee, to report the cases to law enforcement, even though management had been made aware of them.

Shortly after the meeting, Maioriello reported the matter to the local police.

The Times asked the Office for People with Developmental Disabilities why Bishop and Morgese could not say what an assault was and suggested to Maioriello that the allegations should not be forwarded to law enforcement.

The state disputed the framing of the question.

The state was subsequently informed by The Times that a tape existed of the encounter, and shortly thereafter both Bishop and Morgese were removed from their positions. Bishop was reassigned to the central office and Morgese was demoted and sent to a regional office.

Morgese declined to comment, through the agency. In a brief statement, Bishop said she was inspired to get into the field by a developmentally disabled sister.

"I believe that I provided the highest quality leadership," she said, "always guided by respect and dignity for the people we are honored to serve."