Auditors found that the Department of Public Safety used incorrect active duty pay rates to pay those who assisted in the aftermath.
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The department processed 4,354 payments totaling $1.7 million for 1,285 National Guard soldiers, the report stated.
When officials recalculated wage payments to the 1,285 soldiers, the recalculations identified 1,166 (90.7 percent) soldiers were paid in error, resulting in a $38,559 (2.3 percent) net overpayment.
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Auditors said the overpayments could have been used for other Hurricane Matthew disaster assistance related purposes.
"The errors occurred because the National Guard, a division of the Department, did not have procedures in place to ensure the correct rates were used," the report read. "The Department used the State Active Duty system to make the payments. However, review and verification procedures were not in place to ensure that the correct military pay tables (1) were obtained and entered timely in the State Active Duty system."
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State law establishes the active duty pay rate for Department use as:
"The militia of the State, both officers and enlisted personnel, when called into the service of the State by the Governor shall receive the same pay as when called or ordered into the service of the United States, and shall be rationed or paid the equivalent thereof, provided that no officer or enlisted personnel shall receive less than 18 times the minimum hourly wage per day."
Officials have not said if the soldiers would be required to repay the funds, which would average out to about $33 per person.