LOS ANGELES — A federal judge ruled Thursday that Honolulu can continue work on the first three phases of a $5.2 billion elevated rail transit project, but must hold off on construction of the fourth and final phase until certain conditions are met.

The ruling by Hawaii U.S. District Court Judge A. Wallace Tashima effectively secures the $1.5 billion in federal funding Honolulu received from the Federal Transit Administration on Dec. 20 to build the 20-mile rail project from Kapolei to Ala Moana in Honolulu.

It did so by not vacating the FTA's Record of Decision that approved the project's environmental impact statement.

Honolulu Mayor Peter Carlisle, who only has a few days left in office, claimed a victory for rail advocates with the ruling even though hurdles to the project's completion remain.

According to city officials, the decision granted a narrow injunction affecting only one portion of the project.

Work can resume on the first three phases while the city resolves issues around identifying and protecting burial sites near downtown Honolulu.

"This ruling is very reasonable, and is essentially what the city asked for," Carlisle said in a statement.

The rail project has been the subject of several lawsuits in state and federal courts that claim Honolulu and state officials short-circuited laws designed to protect ancient burial grounds as they moved forward with the project.

It also became the biggest topic in the city's recent mayoral election.

Carlisle was defeated in the primary in his bid for re-election but November's runoff election was won by Kirk Caldwell, also a rail advocate.

Former Gov. Ben Cayetano, who ran for mayor on an anti-rail campaign, is a plaintiff in the lawsuit.

While the judge cleared the way for construction to resume on the first three phases, the city will not be allowed to move forward on the fourth phase through urban Honolulu from Kalihi to Ala Moana Center until conditions outlined in a prior ruling from Tashima are met.

In a November ruling, Tashima ordered city officials to more thoroughly evaluate the impacts to Mother Waldron Park in Kakaako, explain why a tunnel under Beretania Street wasn't considered as an alternative route, and identify burial sites on the route.

The decision allows the city to do engineering work and other pre-construction activities on the final phase, but construction can't resume, nor can the city conduct real estate acquisitions for that phase, until it completes the work outlined by Tashima.

City officials said they plan to start construction on the final phase in June 2014.

A Hawaii Supreme Court ruling in August halted construction when it ruled the city and state did not follow the law by conducting archaeological surveys in phases rather than prior to construction on any phase of the project.

The judge's ruling will allow rail officials to complete work requested by the judge and still complete the project in 2019 as planned, according to Honolulu Authority for Rapid Transportation officials.

"This is the news we hoped for," said HART chief executive officer Dan Grabauskas. "These additional studies will be completed next year, well in advance of when construction was scheduled to begin in the city center area."

The HART financial plan assumes Honolulu will issue $1.7 billion of general obligation bonds backed by project revenues, beginning in fiscal 2014, that would be repaid by fiscal 2023.

Other borrowing is to be done on a short-term basis in the form of tax-exempt commercial paper.

Cayetano claims that work can't resume on the the first three phases until the Hawaii Supreme Court issues its ruling in the Kaleikini vs. State of Hawaii case.

"It is inaccurate to say that construction work on Phases 1, 2, and 3 will resume," Cayetano said. "The truth is there is no construction work being done on rail at this time and anytime soon."

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