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UPDATED 9/13/12 4:45 p.m.

The first human remains have been found along the proposed Honolulu rail route, ratcheting up the tension that has gripped the city’s transit project when it comes to the sensitive issue of Native Hawaiian burials.

Members of the Oahu Island Burial Council, a spokesperson for the Honolulu Authority for Rapid Transportation and state officials gathered on Thursday morning around the site where the remains were discovered.

The mood was both tense and somber as construction workers stood guard around a 3-foot by 20-foot long trench that was cordoned off with orange cones. Workers have been digging the trenches along the proposed rail route since April as part of a required archeological survey.

Hinaleimoana Kalu, chair of the Oahu burial council, told Civil Beat that the iwi had been found Wednesday evening.

At this point, it’s not clear if the remains are Native Hawaiian.

UPDATED: In a statement released late Thursday afternoon, state officials said that a single human bone fragment has been found. The State Historic Preservation Division and the burial council have agreed to leave the bone fragment in place for now, and excavation work will continue on the surrounding area.

“Excavation around the bone fragment will provide better information about the cultural layer in which the bone fragment was found and how best to plan for this area,” according to the statement from SHPD.

HART officials also released a statement saying that the finding was anticipated and that they were working with SHPD, the Oahu burial council and other stakeholders to ensure that the iwi was treated “respectfully, with great sensitivity and in accordance with state burial laws.”

“This is not unexpected, in fact we have a protocol in place that is the result of months of collaboration and consultation with all parties, and we will continue to work together throughout this process,” HART said in the statement.

The iwi was found at the corner of Cooke and Halekauwila in Kakaako. It’s the same area that rail opponents have long said there would be problems.

The discovery comes less than a month after the Hawaii Supreme Court ruled that the city and state didn’t follow the law when surveying Native Hawaiian burial sites, causing construction on the rail project to grind to a halt.

In its appeal to the court, asking it to reconsider its ruling, the city said there were “no known existing burials” along the railway alignment in Kakaako, but did note that there’s a “high likelihood” that there are unknown burials in the area.

Rail opponents have said there’s no way the city can build rail through the area without disturbing human remains.

The court could still reconsider the ruling, but so far has not given any indication it plans to reverse itself.

The Native Hawaiian Legal Corporation brought the case on behalf of Paulette Kaleikini, who is a descendant of Native Hawaiians buried in downtown Honolulu where the rail project is designed to run.

David Kimo Frankel, Kaleikini’s attorney, filed a response to the city’s motion for reconsideration Thursday. The Supreme Court has until September 28 to respond to the city’s motion.

Frankel declined to speculate on how the finding of iwi could impact the case. But he did say that it “provides evidence that Paulette Kaleikini had a good basis for filing suit.”

Frankel argued, and the court agreed last month, that a full archaeological survey must be completed before any construction began on the rail route.

The State Historic Preservation Division had signed off on an agreement that allowed the surveys to be conducted in four phases, allowing construction to begin as long as the work had been completed on that phase. But the Native Hawaiian Legal Corporation argued that this could close off options on how to handle any burial remains that were discovered along the way.

The Oahu burial council shared this view, refusing to sign the agreement between the state and city that allowed for the segmented approach.

The council has not taken a position on rail, but has expressed concerns about the proper protection of burials.

“(The burial council) has not made a statement that is for or against rail. Rather, we have a kuleana to fulfill regarding the protection of iwi kupuna and burials and we will fiercely seek to protect that kuleana,” said Jonathan Scheuer, vice chair of the Oahu burial council.

Sen. Daniel Akaka, the only Native Hawaiian ever elected to the U.S. Senate, told Civil Beat that the issue of iwi is very difficult because there are so many burials.

“I would tell you that in Hawaii, and on Oahu in particular, there was a time, in the history of Hawaii, many Hawaiians contracted diseases and many of them died, and many of them were buried all over the place,” he said.

He noted that proper planning for large-scale projects such as rail was critical.

“It’s a warning too to anyone that if you’re going to build any structures like that, they need to bear this in mind and deal with it before you start putting things up,” he said.

—Michael Levine contributed reporting from Washington D.C.