A financially troubled Manhattan restaurateur who sources said had links to the current corruption probe into the NYPD was arrested in Georgia on federal charges he ran a $12 million Ponzi scheme through his sister’s liquor business, officials said.

Hamlet Peralta, who ran the trendy Hudson River Café in West Harlem, was taken into custody near Macon and was taken to court for a brief hearing Friday before he was sent back to Manhattan to face a federal criminal complaint, said a spokeswoman for the U.S. attorney’s office in Georgia.

An 11-page criminal complaint unsealed in federal court in Manhattan on Friday said Peralta, 36, told investors he planned to use their money to engage in a wholesale liquor business but in fact purchased no more than $700,000 in wholesale liquor and used the remainder to pay off earlier investors and cover his personal expenses.

Peralta got his sister’s permission to use the bank accounts of her company, W 125th Street Liquors, to receive wire transfers representing loans from investors, according to the complaint. Peralta’s sister wasn’t charged with any wrongdoing and cooperated with investigators, the court document said.

None of the alleged victims in the scheme was identified. But a source familiar with the case said that one was Jona Rechnitz, a Brooklyn businessman whose name has surfaced in the probe into possible corruption involving high-ranking NYPD officers. The source, who didn’t want to be identified, said Rechnitz’s investment was relatively small, in the $100,000 range, and not anywhere near the $2 million to $5 million other investors allegedly lost.

Both Rechnitz and another prominent businessman, Jeremy Reichberg, have figured in the probe of the officers, who are being looked at for possibly receiving illegal gifts and gratuities. Neither Rechnitz nor Reichberg have been accused of any wrongdoing.

advertisement | advertise on newsday

Sources have said the investigation began with a probe into whether Norman Seabrook, the head of correction officers union, invested millions of dollars of the union’s funds into a hedge fund in return for receiving benefits such as trips overseas with his friend and former high-ranking police official, Philip Banks.

Both have denied any wrongdoing and have not been charged with any crimes.

The sources said that investigation then eventually merged into one involving Peralta’s alleged Ponzi scheme. Both Rechnitz, Reichberg and Peralta were friendly with a number of the police officers who have figured in the overall investigation.

On Thursday, NYPD Commissioner William Bratton placed two high-ranking officers on modified status and transferred two others as a result of the federal-city investigation.

Peralta’s troubles and his alleged scheme may have been a key reason the FBI was led to the NYPD officials, according to one law enforcement official. Peralta reportedly entertained cops at the restaurant.

Get the Newsday Now newsletter!

The best of Newsday every day in your inbox.

The Hudson River Café had a reputation for being a nice river-view eatery with a Latin flavor. But it ran into financial trouble and has closed. A group of waitresses and bartenders filed a federal lawsuit in 2012 for back wages and tips against Peralta and the cafe. Peralta owes the former staffers $250,000, said their attorney Bruce Menken of Manhattan.

But Peralta’s arrest makes it unlikely the workers will see any money, Menken said.

Peralta recently pleaded guilty to a state charge of offering a false instrument for filing in connection with a tax document related to the cafe, said a spokeswoman for the Manhattan district attorney’s office. Peralta agreed to pay back $350,000 and received a conditional discharge.