Archaeological excavation for ancient human remains will occur at more than 200 locations in the downtown and Kakaako corridor of Honolulu’s $5.5 billion rail route.

The city has identified 212 excavation sites within the final and most controversial phase of rail construction.

Areas marked for excavation — some under existing buildings — include the locations for future transit stations, preliminary engi­neering plans show. Much of the digging will also occur near the column foundations for the elevated guideway.

Field work for the archaeological inventory survey in the fourth phase is expected to begin this fall, said Hallett Hammatt, president of Cultural Surveys Hawaii, which will be conducting the surveys for the city.

“On this scale, I would say it’s never been done before in Hawaii,” Hammatt said in a recent public meeting regarding the fourth phase.

The city has acknowledged the high likelihood that native Hawaiian remains, iwi kupuna, will be found along the route. The city’s current plans are to conduct surveys in four phases along the planned route. No remains were found in the first phase, largely in undeveloped agricultural lands, but the fourth phase has the most development.

Construction from Middle Street to Ala Moana Center is expected to begin in 2014.

The archaeological survey will employ several methods. Crews will use ground-penetrating radar to map the subsurface where conditions might indicate a burial, Hammatt said.

Crews might also use “historic human remains detection dogs” to sniff out remains.

More extensive open excavation will be used if further analysis is necessary.

Hammatt said about 96 percent of the excavation will be for utility relocation.

“We did a rough calculation,” Hammatt said. “The other 4 or 5 percent is going to be the stations and the columns.”

Hammatt said many of the utility relocations will be shallow, and that the depth may vary depending on the utilities involved.

The fourth, final phase was the central issue in a lawsuit that attempted to halt the rail project until an archaeological inventory survey was completed for the entire 20-mile route.

Paulette Kaleikini, represented by the Native Hawaiian Legal Corp., argued that state law prohibits a project to be divided into phases when it comes to archaeological studies, as with environmental impact statements.

However, Circuit Judge Gary Won Bae Chang dismissed the suit, stating that the laws governing archaeological surveys and environmental impact statements are separate. Archaeological laws do not specifically prohibit the phasing of projects, he said.

Kaleikini and her attorneys have indicated they will appeal. Many residents against the rail transit project pinned their hopes on that lawsuit.

In response to concerns raised by the community, the city decided to expedite the fourth phase’s survey.

But it is still coming too late, said Kehau Abad, chairwoman of the Oahu Island Burial Council’s rail project task force.

“Big decisions like route and technology have already been made,” Abad said. “These studies should have been done as part of the alternatives analysis.”

If remains are found or identified during the survey process, a “treatment plan” on how to deal with the remains can be worked out with the descendants within 90 days of the discovery, Abad said. The treatment plan could mean preserving the remains in place, or relocation.

However, there could still be “inadvertent discoveries” of burials during actual construction. At that point, the window of time to decide what to do with the remains is much smaller, according to the agreement between federal and state agencies that outlines the protocol for historic preservation.

If a burial is found during construction, the state Historic Preservation Division has only one day to make a determination for a single burial, and two days for multiple burials. The agreement allows for a three-day extension for both cases, “recognizing the extent of the project and the sensitivity of any discoveries.”

That is why Abad is urging city planners to conduct more surveys in certain areas, particularly south of Halekauwila Street in Kakaako.

“The council is set up purposefully to allow for cultural descendants to have their appropriate input in the process,” Abad said. “The better the study is up front, the more likely you’ll be able to find as many of the burials you can. If you have a very small sampling of the area, a light-touch investigation, there will be less of the iwi kupuna being treated in this more careful manner.”

In the past, some native Hawaiians have had no objections to iwi kupuna being relocated. When Walmart planned its Keeaumoku complex in 2003, some potential descendants preferred to have remains moved to a quieter, drier area of the parcel. Kaleikini at the time filed a lawsuit to stop the development, but the ultimate ruling favored  Walmart.

Hinaleimoana Falemei, vice chairwoman of the Oahu Island Burial Council, said the council does not want to be construed as anti-development.

She agrees that the state needs an economic stimulus, but argues that the Burial Council has a responsibility to the native Hawaiian community. She said that if remains are found, the Burial Council will only appear as obstructionist.

“It always ends up being about negotiating with the Hawaiians, and the Hawaiians are looking like we’re stopping everything,” Falemei said. “What would happen if we said we’re building rail through the Kaneohe memorial cemetery, and that we’re going to compromise or move the remains there? Do you think the public would receive that?”

Falemei said the council is trying to be proactive, and that the city should pay attention to concerns so the project will be less encumbered in the future if there are any necessary changes that need to be made.

City transportation officials have said that if remains are found, the guideway’s columns can be moved to avoid disturbing the graves. Pete Manaut, a Carlsmith Ball LLP attorney who represented the city in the recent Kaleikini case, said the city would also consider changing the alignment, which is why it is conducting the survey as early as this year.

“The potential for iwi displacement is far greater in this project,” Falemei said. “But there’s also the precedent that it sets, saying that native Hawaiian concerns are going to be secondary, that iwi kupuna concerns are secondary.”