Nassau County Comptroller George Maragos, after a nearly six-month audit, has agreed to issue final payment to a company whose $12.5 million storm cleanup contract has been the focus of federal and local criminal investigations.

Maragos said Tuesday that his office found no evidence of fraud or major errors in the final $386,380 claim by VIP Splash Waterways Recovery Group Inc. from a contract amendment finalized in July.

When payment is issued later this week, it will formally complete a pact to clear superstorm Sandy debris from South Shore waterways that was first approved by county legislators for $4 million in November 2013. For much of the last two years the contract has been the subject of controversy over how it was awarded, and because of political contributions made by VIP Splash to County Executive Edward Mangano’s chief deputy, Rob Walker.

The U.S. attorney’s office for the Eastern District and the Nassau County district attorney issued subpoenas related to the contract. Newsday reported in 2015 that VIP Splash was incorporated just days before the county first solicited bids for the work, and that the company contributed to Walker’s political club on the day in 2014 that Walker signed an initial $8.2 million contract amendment.

In announcing his audit of the contract last summer, Maragos, a Republican-turned-Democrat who is running for county executive this year, cited the criminal investigations as well as “whistleblower” complaints about VIP Splash’s work.

“There’s discomfort, of course there is,” Maragos said in approving claims tied to a contract under investigation. “But I think we went the extra mile and increased the diligence to ensure that we were completely satisfied. We couldn’t discern any reason to withhold payment.”

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The Comptroller’s office used field audit staff to interview administration officials, VIP Splash representatives and residents who were critical of the company’s work, Maragos said. They viewed photos and looked at weight and measurement data from debris removal claims.

“They found no issues and were comfortable in recommending payment,” Maragos said.

A representative for the Eastern District declined to comment Tuesday on the status of its investigation; the Nassau district attorney’s office said only that its probe was ongoing.

Walker’s attorney, Brian Griffin, has said that Walker “has complied with all legal obligations and acted in an appropriate and transparent manner.”