NEW YORK — The glittering, steel and glass domed rail hub had seemed for years to be the only thing that was going right at ground zero.
Lately, not so much.
The World Trade Center rail station — a planned architectural masterpiece with steel ribs jutting like a bird’s wings from the dome, a retractable skylight and a vast, naturally lit concourse — is currently hundreds of millions of dollars over budget and five years behind schedule.
The delays are creating a domino effect, slowing construction of the Sept. 11 memorial and most other projects on the problem-ridden 16-acre site.
The Port Authority of New York and New Jersey, the owners of ground zero and the agency building the hub, is expected to announce another re-design of the project this week along with new cost estimates that put the price tag at around $3 billion, more than $500 million over its original budget.
But reports prepared for the federal government — which is funding the terminal with post-Sept. 11 money — show that problems managing the project were foreseen at least two years ago. The transportation consultant reports warned of management problems, cost overruns and delays at the hub going back to 2006, less than a year after construction began.
The rail terminal would replace a PATH commuter rail hub that was underneath the trade center’s twin towers before Sept. 11, 2001, and a temporary station that opened in 2003. The PATH trains take commuters between New York and New Jersey.
The design by Spanish architect Santiago Calatrava has won praise. It was called ‘‘the single note of optimism in a cesspool of cynicism and politics’’ in a New York Times architecture review in 2004, and perhaps a more moving Sept. 11 tribute than the memorial.
The hub would also include high-end shops and underground concourses connecting passengers to more than a dozen subway lines. Business leaders have said the terminal would attract corporate tenants to the five planned skyscrapers and the financial district.
Because the hub is located in the middle of ground zero, its problems affect a maze of interconnected skyscrapers, the memorial, city streets and vehicle security center planned for the site.
The federal consultant reports assessing risks on the project are prepared every three months for the Federal Transit Administration, which funded the hub with an initial $1.9 billion grant.
In July 2006, the report by the Carter & Burgess consultants concluded the hub had less than a 10 percent chance of being on budget. Every three months, the consultants issued new reports that estimated delays as high as 15 months. By early 2008, the consultants said it was less than 5 percent likely to be on budget.
Failure to make timely decisions, delays in procuring contractors, constant design changes and the extra cost of paying staff for a longer-than-expected job were repeatedly cited as indicators of budget and schedule problems in 18 months of reports reviewed by The Associated Press after a Freedom of Information Act request.
‘‘This is a large, schedule-driven project with an aggressive design schedule,’’ the report read in July 2006, referring to ‘‘rushed,’’ incomplete design documents that were causing delays.
‘‘Delays have been experienced during construction of the early work packages, for example, due to lack of firm schedules provided to contractors and slow processing of change orders,’’ read a notation made in four separate reports filed last year.
A report dated last fall said a ‘‘lack of timely, proactive decisions by senior management’’ could cause further delays.
Experts said the reports show longtime oversight problems at the complicated project. ‘‘It probably does raise some red flags,’’ said Jeffrey Zupan, an engineer and senior transportation analyst at New York’s Regional Plan Association.
Port Authority spokesman Stephen Sigmund said the agency acknowledged problems with the project in a June report, ‘‘and have since moved forward with a new way of doing business on the site in close coordination with the (federal government) and other partners. And we are producing positive results.’’
Sigmund said the agency has a new executive director and a new director of capital construction in charge of the hub and the trade center site, but the changes weren’t made specifically because of issues with the rail hub.
Calatrava said in a statement Monday that over the past two months, his team has worked to ‘‘review the scope of the project in both functional and technical terms’’ in a way that conforms to its current budget and coordinates construction with other projects on the site.
‘‘It has always been my goal to deliver a beautiful and practical facility for lower Manhattan,’’ Calatrava said. ‘‘In its revised state, the project retains all of its fundamental beauty and functionality and will serve New York well in the years to come.’’