Nearly 40 years after New York emptied its scandal-ridden warehouses for the developmentally disabled, the far-flung network of small group homes that replaced them operates with scant oversight and few consequences for employees who abuse the vulnerable population.

A New York Times investigation over the past year has found widespread problems in the more than 2,000 state-run homes. In hundreds of cases reviewed by The Times, employees who sexually abused, beat or taunted residents were rarely fired, even after repeated offenses, and in many cases, were simply transferred to other group homes run by the state.

And, despite a state law requiring that incidents in which a crime may have been committed be reported to law enforcement, such referrals are rare: State records show that of some 13,000 allegations of abuse in 2009 within state-operated and licensed homes, fewer than 5 percent were referred to law enforcement. The hundreds of files examined by The Times contained shocking examples of abuse of residents with conditions like Down syndrome, autism and cerebral palsy.

At a home upstate in Hudson Falls, two days before Christmas in 2006, an employee discovered her supervisor, Ricky W. Sousie, in the bedroom of a severely disabled, 54-year-old woman. Mr. Sousie, a stocky man with wispy hair, was standing between the woman’s legs. His pants were around his ankles, his hand was on her knee and her diaper was pulled down.