Suffolk County Comptroller John Kennedy is seen in this undated...

Suffolk County Comptroller John Kennedy is seen in this undated photo. Credit: Joseph D. Sullivan

The Long Island Women’s Empowerment Network will be terminated as the operator of Suffolk County’s largest homeless shelter in Brentwood, after officials found that the nonprofit overcharged the county by $3 million over a two-year period.

County Comptroller John Kennedy uncovered the overcharges in an audit that started in August and covered a 23-month period in 2013 and 2014.

Kennedy pressed social services officials to take emergency steps to end the contract. He also has referred his findings to the Suffolk District Attorney Thomas Spota for possible criminal prosecution.

“Shortly after our audit started, Social Services realized it was an out-of-control mess,” Kennedy said.

The group’s top official, president Julie Levine, has been barred from entering the shelter since October, according to the comptroller’s office. A formal termination notice is expected to be announced Wednesday at news conference in Hauppauge.

Levine and the network’s attorneys did not return repeated calls for comment Tuesday.

The social services department has taken over the operation temporarily. The department is using many of the existing staff so that the shelter’s 117 adults and 287 children can continue to receive services without interruption, according to Kennedy’s office.

Another nonprofit provider is expected to be named soon to take over operations.

Kennedy found that the Long Island Women’s Empowerment Network overcharged $1.099 million using a higher daily rate of $58.73 per person, a rate higher than permitted as a Tier II shelter, which provides food and other support services.

The nonprofit never got state approval for the designation, Kennedy said. Without it, the charge would have been $46.18 per person a day.

Auditors also found $2.237 million in spending claimed by the nonprofit that the comptroller disallowed. The largest portion was for maintenance, security and housekeeping services that the nonprofit contracted out for improperly without county approval, Kennedy said.

The network spent $866,433 more than the $2,089,408 the county had included in the shelter’s $6.6 million budget to fund that work in-house.

The comptroller also said Levine in 2014 used the nonprofit’s debit card to spend $2,361 at Tropical Togs Hotel in South Carolina and $2,774 at the Bonwit Inn Restaurant in Commack.

Kennedy said that during the audit, he notified the nonprofit that it had to refund the $1.099 million within 15 days. The agency responded that it was suffering financial hardship and could not pay, Kennedy said.

In January, the county withheld $446,093 in payment to the network and an additional $200,000 in February and it will hold back $453,443 from bills officials expect from the network this month, Kennedy said.

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