New York auditors found that the state’s Medicaid system processed nearly 10.8 million pharmacy claims using expired billing authorizations and that oversight of county probation departments left inconsistent supervision practices, according to two audits highlighted Monday by state Comptroller Thomas DiNapoli.
The Medicaid audit examined fee-for-service claims from January 2020 through December 2024. The separate probation audit covered January 2019 through April 2026. Both address statewide systems that include Finger Lakes providers or county departments, but neither report identifies a regionwide total for the findings.
The findings describe weaknesses in administrative controls and a nonrandom sample of probation cases. They do not establish that all affected Medicaid claims were fraudulent, that patients received improper care, or that the sampled probation rates apply to every county. The agencies disputed or qualified parts of the auditors’ conclusions and described steps they are taking.
Medicaid claim identifiers
Medicaid uses electronic transmitter identification numbers, or ETINs, to identify providers and service bureaus that submit fee-for-service claims. Providers must maintain active, certified affiliations for those identifiers. The Department of Health’s eMedNY system processed 10,772,402 pharmacy claims associated with 720 expired ETIN affiliations, auditors found. Payments on those claims totaled about $1.37 billion.
The audit found that pharmacy claims were not subject to a system edit that checks for expired affiliations. Health officials said they had left that edit out because medication delivery is a critical service. Auditors said the department nevertheless had data it could have used to monitor expired identifiers; more than 80% of the affected pharmacy claims had service dates over a year after the affiliations expired.
For non-pharmacy services, auditors identified another 4,932 claims, totaling about $394,000 in payments, submitted using 63 identifiers that were expired or had never been affiliated with the billing providers on the service dates. In all, the audit counted 783 identifiers tied to the nearly 10.8 million claims flagged in its findings.
Auditors also examined 242 service bureaus whose identifiers appeared on claims. They found 84 with Medicaid enrollment IDs that remained inactive during the audit period and three with no Medicaid ID. One bureau excluded from Medicaid participation had an identifier appear on 30,415 claims totaling $1.4 million after its exclusion. The report does not conclude that all those payments were improper; auditors called for the claims to be reviewed.
The Department of Health said it is exploring how to update the expired or missing affiliations and needs a process to improve monitoring. It accepted a recommendation to review claims tied to the excluded bureau and said any claims found inappropriate would be referred to the Medicaid inspector general. Auditors also recommended documenting the rationale for certain existing claim checks.
County probation supervision
The Division of Criminal Justice Services oversees and funds 58 probation departments serving New York’s 57 counties and New York City. Auditors visited six county departments and reviewed 105 selected adult case files. In 20 files, they found fewer required contacts with probation officers than the person’s risk level called for. Among 101 files with a court-ordered drug or alcohol condition, 27 showed no drug or alcohol test during the review period.
Those case files were selected through a nonstatistical, risk-based approach; the percentages are findings from the six visited counties, not statewide estimates. Auditors also surveyed 53 other counties and received 48 responses. Of those, 41 said the state agency did not visit annually or more often to monitor their departments, while 13 wanted more visits. The report said county practices varied in risk ratings, caseloads, training and supervision of court-ordered conditions.
DCJS said sentencing courts—not the state agency—set individual probation conditions, and county departments supervise people on probation. It argued that a uniform caseload cap could ignore differences in case complexity and that the audit did not measure statewide recidivism or other public-safety outcomes. The agency said it established a new site-visit protocol in February, with two county reviews planned in 2026 and four annually afterward, and would examine documentation of testing and staff-related critical incidents.
Auditors acknowledged that counties need flexibility, but said the state can give clearer guidance and verify compliance without rewriting court orders. The report recommends evaluating monitoring practices and drug- and alcohol-testing guidance. DCJS is required to tell state leaders within 180 days what steps it took on the recommendations or why it did not implement them.
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