The site was discovered by a park supervisor after the Peconic River bank eroded in stormy conditions last week, Newsday reported Thursday.
Archaeologists said they found bones from at least two people believed to be American Indians buried at the site during the Early Woodland period, from 800 B.C. to A.D. 800. They also said they found several artifacts, including a pipe and fragments of a bowl.
The remains were being examined by a forensic anthropologist.
"The bones were in small pieces," David Thompson, vice president of the Suffolk County Archaeological Association, told Newsday. "They were obviously burnt. There were charred pieces of skull and small pieces of a jawbone.
The fact that they were cremated is a holdover from a culture that immediately preceded the Early Woodland, which was called the Transitional Culture.
Officials said they were uncertain what will happen to the site.