Nassau County Comptroller George Maragos said he will conduct an "extensive" audit of the county's homeless shelter system, after previous audits, including one released Monday, uncovered shoddy bookkeeping.

The latest audit showed that Freeport nonprofit Eager to Please Inc. routinely underpaid and delayed paychecks to employees from 2012 to 2014.

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"The audit findings are not only very disturbing but may underscore more extensive issues with the quality of housing provided to our neediest residents," Maragos said in a statement Monday about the 23-page report. "We intend to open a more extensive audit of the homeless shelter industry on the quality of shelter being provided with taxpayer money."

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Eager to Please paid 11 employees between $11.50 and $14.50 an hour, less than the county's current Living Wage Law of $15.50 an hour, according to the audit. The underpayments totaled $4,899 over two years. The report stated that on some occasions employees waited from 27 days to nearly two years for their paychecks.

The shelter will take "corrective measures . . . to rectify the areas where we were not in compliance," wrote executive director Levada Felder in a letter to Maragos' office. She said the agency will pay wages owed to employees and upgrade its payroll system. No one from the shelter was available for comment Monday.

Maragos spokesman Jostyn Hernandez said his office will audit the county's more than 20 nonprofit homeless shelters to ensure they are in compliance with county wage laws and delivering the services for which they are paid by the county.

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In January, Maragos' office found Hempstead shelter Peace Valley Haven had underpaid employees about $120,000 over a two-year period. Shelter officials told auditors they have since increased their hourly wage to $17 -- $1.50 more than the county requires.In 2013, Maragos' office found two Hempstead shelters -- Bethany House and Glory House Recovery -- had underpaid employees $10,000 for more than a year.