Police and more than 100 firefighters responded to the residence on Centre Island Drive in Centre Island just after 10 a.m.
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There are no hydrants on the island, so firefighters had to rely on tanker trucks and a fire apparatus boat that helped with water from the bay.
"We had to use water from our boat," Bayville Fire Chief Dave Caso said. "It has a pump on it. We brought the water up to the scene from the bay."
Caso said it took several hours to get the fire under control.
The victim, referred to by police as a senior citizen, was reportedly the homeowner. He was found inside the home.
Nassau police Detective Lieutenant Stephen Fitzpatrick said the man lived in Queens but visited the house for vacations.
His identity has not yet been released, but police say they have spoken to his family.
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Police say the fire was extremely strong, but the cause is still unknown.
"The source of the fire was to the center of the house," Fitzpatrick said. "The intensity of the fire is what's concerning to us. We don't know what the source of the fire was. It's not in the area of the house such as the kitchen that would be able to fuel that fire to make it that intense...We don't know whether it's suspicious or it's undetermined right now."
An ATF specialist who specializes in identifying sources of fires is also at the scene.
People who know the victim described him as "eccentric."
According to online real estate website Zillow, the house is listed as pre-foreclosure. It was bought in March 2010 for $2.4 million.
The investigation is ongoing.
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