ALBANY — The state agency in New York that investigates abuse and neglect of disabled people in institutional care refused to hand over thousands of records to auditors, the state comptroller’s office said Monday, complicating efforts to determine whether the agency is fulfilling its mission.

State auditors had requested access to nearly three years of reports on alleged abuse and neglect of people living in state institutions, group homes and state-licensed facilities. Instead, the Justice Center for the Protection of People with Special Needs provided records covering just 6,250 cases — less than 8 percent of the 82,000 incidents reported to a state abuse and neglect hotline.

State Comptroller Thomas DiNapoli said the Justice Center’s decision to withhold so many records is “troubling” considering the agency’s critical role. Democratic Gov. Andrew Cuomo created the agency in 2012 to root out abuse and neglect of the state’s most vulnerable residents.

“If they’re doing their job … it would be in their best interests to have an independent verification of the work,” the Democratic comptroller told The Associated Press on Monday. “Their resistance does seem to raise additional questions.”

The AP obtained a copy of the audit from the comptroller’s office, which plans to release the report publicly on Tuesday. In its formal response, the Justice Center argued state law requires it to withhold records that pertain to allegations of abuse or neglect that are still under investigation as well as those deemed unsubstantiated.

“The Justice Center provided state auditors with access to all investigative records and information permitted to be disclosed under state law,” the agency said in a statement. It added that “strong confidentiality provisions” limit access to reports of allegations that are found to be unsubstantiated.

DiNapoli said the agency had the authority to release the records to auditors, whom he noted routinely inspect sensitive state records. He is now seeking legislation to clarify the law to give auditors access going forward. He noted the agency also has refused to release certain records to Disability Rights New York, a nonprofit granted federal authority to monitor efforts to protect disabled residents in the state. DRNY is suing the Justice Center over its lack of access to the records.

DRNY Executive Director Timothy Clune said the audit highlights “a lack of transparency and oversight.”

An AP review of the Justice Center last year found that it investigated only six of the nearly 1,400 cases of developmentally disabled people who died in state care from June 30, 2013, to May 31, 2015.

In an analysis of the records made available, auditors found several instances of sloppy paperwork by the agency. Three workers with past incidents of abuse or neglect were not added to a registry of staffers prohibited from providing direct care to patients. All three had worked in facilities that are not operated by the state and are no longer employed.

The audit also found records of 223 substantiated cases of abuse or neglect that were missing key dates, such as the day of the allegation.

The Justice Center said it upgraded its internal controls to improve its record keeping while the audit was underway.

Longtime disability advocate Michael Carey had sought the audit and said he was disappointed DiNapoli didn’t recommend significant changes at the Justice Center, such as requiring employees to call 911 in the event of a problem or requiring allegations of abuse or neglect to go to prosecutors for independent review.

But he said the agency’s refusal to release records to auditors “reveals wide-scale obstruction by the Cuomo administration.”