The search for a Babylon man missing since the fishing boat carrying him and two others capsized Tuesday near Fire Island Inlet was suspended Wednesday night and will resume Thursday morning, Suffolk police said.

Roberto Vasquez, 50, was aboard the 21-foot boat with Carlos Hernandez, 36, of Wyandanch, and Erik Flores, 30, of Amityville, when the vessel overturned early Tuesday night in waters just west of the Robert Moses Causeway, about 200 yards south of Cedar Beach, the Coast Guard and Suffolk police said.

Search teams from the Coast Guard and the Suffolk police marine bureau began looking for the three men after a commercial fishing vessel called 911 to report the capsized boat at about 6 p.m. Tuesday.

A short time later, crew members on the vessel plucked Flores from the water and a Coast Guard crew pulled Hernandez to safety near the capsized vessel, officials said.

The Coast Guard said the search has covered 388 square nautical miles over 35 hours.

Wednesday night, officers with the marine bureau said strong ocean and bay currents hampered the search.

Suffolk police said “periodic checks” will continue through the night with marine bureau officers expected to resume the search Thursday morning.

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Flores and Hernandez told authorities Vasquez never surfaced after their boat flipped, Coast Guard officials said. The pair eventually were transported to Good Samaritan Hospital Medical Center in West Islip where they were treated for exposure and released.

They told authorities two waves crashed into their boat, flipping it. The last time both saw Vasquez, his companions said, the Babylon man was underneath the capsized boat, his hand holding onto the hull, said Lt. Raymond Epp, of the marine bureau.

A marine bureau officer, Jack Brehm, swam to the hull in hopes of finding Vasquez in an air pocket, Epp said.

“He was knocking on it,” Epps said of the officer’s efforts, “and didn’t hear anything back.”

NYPD aviation and dive teams assisted with the search.

The capsized recreational vessel was towed to the Captree State Park marina in Babylon, the Coast Guard said.

Anyone with information about the missing boater’s location should call the Coast Guard Sector Long Island Sound Command Center at 203-468-4401.

With Gary Dymski