A state judge sided with the city yesterday, dismissing a lawsuit that sought to halt the $5.5 billion rail transit project until the city completes a survey of ancient Hawaiian burial sites along the project’s entire 20-mile route.

Circuit Judge Gary Won Bae Chang said it is acceptable for the city to conduct the required archaeological inventory surveys in phases, as it progresses to the next construction phase.

Lawyers for the Native Hawaiian Legal Corp., which represented plaintiff Paulette Kaleikini, said they will appeal.

Kaleikini claims her ancestors are buried in the Kakaako area, where the rail line’s fourth phase will be built, and that the burials could be disturbed. Her lawyers argued that an archaeological survey is like an environmental impact statement and must be completed for the whole project before construction on any portion can begin.

But Chang said state laws governing archaeological and environmental protection are distinct.

While environmental laws prohibit breaking up a project and its EIS into phases, archaeological laws do not, he said.

The judge also pointed out that federal laws governing the protection of archaeological and historical property allow segmenting construction projects and approvals into phases.

The city’s victory comes at a time when high-level federal transportation officials visiting Honolulu praised the handling of the project.

"This project is too important at this point for the jobs that will be provided for Hawaiians, for the model transit program that this will create on the island," U.S. Secretary of Transportation Ray LaHood said yesterday. He called the project a "jobs program."

LaHood and Federal Transit Administration Administrator Peter Rogoff met yesterday morning with local officials, including Hawaii’s congressional delegation and Gov. Neil Abercrombie.

LaHood said he will not be involved in local debates about "bills that have been introduced or ways to finance things."

The city is expected to submit an updated financial plan to the Federal Transit Administration before summer.

LaHood was asked about concerns that the city is spending local tax money without federal funding commitment.

The city is seeking $1.5 billion in federal funding, and that commitment is not expected until later this year or early next year.

Funding is still subject to congressional approval.

"Everything that has been done here has been done correctly," LaHood said. "We don’t do projects unless they’re done by the book. … This project is being done by the book, which is the way these elected officials want it done."