A tribal medicine man from the Shinnecock Indian Nation was legally transporting taxed cigarettes from his state-licensed South Carolina distribution company to the Southampton reservation in July 2012 when he was stopped on the Long Island Expressway by Suffolk County police.

Six years later, after federal prosecutors declined to pursue the case, the FBI returned $34,623 in cash confiscated during the stop, but never told Jonathan Kent Smith, a Shinnecock member and shop owner, what happened to the more than 2,000 cartons of cigarettes he'd been transporting, he said.

Now, newly released FBI documents show that the cache of cigarettes was destroyed. As a result, Smith told Newsday he was forced to close his business for a year and laid off employees because of the loss of more than $130,000.

Newsday obtained the FBI documents through a Freedom of Information Act request filed with the agency in 2018, with Smith’s authorization to release his file. The FBI in its response noted that it "deleted" some 338 pages from Newsday’s document request and the documents it did produce are heavily redacted. Smith saw his FBI file for the first time when Newsday shared it with him.

The documents show a "contraband cigarette trafficking" investigation involving Smith was begun in October 2012, following the July stop. Documents also show the operation was begun after a person listed in the documents as "Chief White" told authorities a source tipped him about the pending shipment. The Suffolk district attorney’s office was briefed on the proposed stop, according to police records included in the file.

According to a civil lawsuit Smith filed in 2012 as part of his attempt to recoup his property and included in the FBI documents, police told him he had been "swerving all over the road," which he denied. The defendants in the suit were two Suffolk County police officers, including one who worked on a federal crime task force and is now a Suffolk legislator, alleging illegal search and seizure and deprivation of civil and treaty rights.

The civil case was ultimately dropped. "I ran out of money," Smith said.

Contents of the rental truck were confiscated by Suffolk police and eventually transferred to FBI custody as part of its investigation, records show. Police at the scene, including now-Suffolk County Legis. Robert Trotta (R-Fort Salonga), then a Suffolk police officer assigned to a federal crime task force, seized three pallets of cigarettes valued at more than $100,000 and more than $34,000 in cash.

Trotta asserted in an interview that the seizure was "100% by the book." Trotta and another Suffolk officer, Vincent Fredrico, were the only named defendants in Smith’s suit. A Suffolk police spokeswoman said Fredrico no longer works for the department, and attempts to reach him were unsuccessful.

FBI records show Smith produced, among other documents, a full inventory of the truck, including receipts showing the taxes he paid for the cigarettes, and his South Carolina distributor's license, which allowed him to "purchase, sell, and distribute manufactured tobacco," according to the documents.

"They had everything needed to know it was not illegal and they still took it and destroyed it," he said of authorities seizing his cigarettes and cash.

Trotta noted he was removed from the federal crime task force shortly after the traffic stop and wasn't involved in custody of the inventory.

"I had nothing to do with that — I was transferred a week later. I don’t know what the feds did with them," he said of the cigarettes.

Documents indicate the cigarettes were transferred to federal custody during Superstorm Sandy, which hit in October 2012.

In a report included in the FBI documents, an officer on the scene of the 2012 traffic stop said a second officer, "after conducting a license check, advised me that Smith was on parole for a gun charge."

Smith, in an interview, said that claim was false. "It's all a big lie," he said. "I can't even wrap my head around it." A Newsday check of records found no such conviction of Smith for a gun or any other criminal offense.

The recently obtained FBI documents show, as Newsday has previously reported, that a check for $34,623 was sent to Smith in January 2018, providing no information about the investigation or its conclusion. The documents show the probe was closed in 2017 after prosecutors in the Eastern District of New York declined to pursue the case. John Marzulli, a spokesman for the office, declined to explain why.

The documents also show that the federal government in 2016 destroyed the 2,078 cartons of cigarettes seized from Smith in what it termed an "evidence burn." The document explains, "The chains of custody cannot be located and may have been inadvertently destroyed."

FBI spokesman Martin R. Feely said the agency would not comment.

Trotta in 2018 told Newsday he was "shocked" the FBI returned the cash he seized from Smith, blamed police and government mismanagement and added, "I’m surprised they didn’t give them [Smith] back their untaxed cigarettes."

The FBI documents show Smith paid taxes on the cigarettes, most of which were purchased from a Sam's Club.

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