Workers are almost done building the rail system’s Pearl City-based high-tech operations center — a milestone that rail leaders touted Thursday — but the deal for the city to own the land under that site still isn’t done and at least one key rail official is concerned about how that might affect the project.

The 43-acre facility, next to Waipahu High School, Leeward Community College and Pearl Harbor, will serve as a state-of-the-art nerve center of sorts, where rail employees will control and take care of the elevated rail system’s driverless trains, guiding the cars on automated tracks into a large hangar bay for inspection and repair.

It sits on what’s known as the former Navy Drum site, owned by the Department of Hawaiian Home Lands. Some 80 percent of the operations center has been built since construction started in 2013, and the whole facility is slated to be ready in 2016, rail officials say. The joint venture Kiewit Kobayashi secured a $195 million contract to build the center in 2011, but rail officials say those costs have since swelled to about $275 million, with the bulk of those added costs coming from delays and design changes to automate the track system there. Contingency dollars are covering the added cost, they say.

“When I became mayor in 2013, this site was just a bunch of dirt,” Mayor Kirk Caldwell said during a press briefing and construction tour Thursday. “I wish this same pace continues for the rest of the project. What is happening out here is what we’d love to see along the rest of the route.”

The city doesn’t yet own the land underneath the operations center that’s taking shape, however. Officials say they’ve agreed with DHHL terms on a land-swap deal in which the city would get the Navy Drum site in exchange for land at Varona Village and in Ewa Beach, but that the U.S. Department of Interior will have to give final approval. The Honolulu Authority for Rapid Transportation doesn’t know when that might happen.

In the meantime, HART finally secured last year a detailed licensing agreement with DHHL giving the city control of that property after federal officials had pressed HART for about three years to execute such a deal.

“Everything’s been concluded, but the final step is with the Department of Interior,” HART Executive Director Dan Grabauskas said of the land-swap deal Thursday while helping to guide the media through one of the operations center’s four buildings. The licensing agreement gives the city a 65-year occupancy permit, he said. The deal to eventually own the land “is going to close, but it’s just taking more time,” he said, adding, “But we do have a lease for 65 years to be here. … All thumbs are up. It’s just a matter of process.”

The main thing that the Federal Transit Administration, which is working with the city to build rail, looks for “is a significantly long-term commitment, so 65 years certainly meets that criteria,” Grabauskas added. The fact that the center is almost done won’t affect terms with DHHL, he said. “Negotiations are done. It’s really just paperwork at this point.”

However, former U.S. Rep. Colleen Hanabusa, who joined HART’s board of directors last summer, said she doesn’t think it’s a sure thing that federal officials will approve the land swap. The Interior Department is considering adding two new rules pertaining to the Hawaiian Home Lands Recovery Act of 1995 that would have federal authorities weigh whether certain land exchanges are in the best interests of DHHL beneficiaries, she said.

If the Interior Department adopts those rules, Hanabusa added, it would directly affect the city’s pending land swap with DHHL.

“It’s not necessarily a slam dunk that they’re going to find this in the best interest of the beneficiaries,” Hanabusa said. The Navy Drum site that DHHL would relinquish, overlooking Pearl Harbor, is scenic, she pointed out. If the Interior Department doesn’t approve, DHHL would likely have to be compensated in some other way, although she wasn’t sure how.

For years rail opponents criticized the city as prematurely pushing ahead with the project — including a decision to allow construction companies to start building before the project had all of the proper federal permits, a move that cost rail millions of dollars.

However, HART officials as far back as 2012 have said that starting construction on the rail operations center before the city owned the land was not a case of jumping the gun. On Thursday they pointed to the center’s near completion as a bright spot for the project, even as rail faces more potential cost overruns and schedule delays of more than a year.

“We need to stay the course. We need to be steadfast in our support of seeing it completed, however long it takes,” state Sen. Clarence Nishihara (D, Waipahu-Pearl City) said at Thursday’s press briefing.

Hanabusa said the Interior Department likely would not decide on those pending rules before December.