The city’s project to build a ferry terminal on the southern tip of Manhattan is $55 million over its original budget and almost two years behind schedule, earning it the moniker “the Little Dig.”

The New York Sun reported last month that a sister terminal across the harbor on Staten Island is $31 million over budget, in part because of an indictment, a bankruptcy, and other problems with contractors.

Delays at the Whitehall Ferry Terminal and Peter Minuit Plaza project site began shortly after a groundbreaking September 25, 2000, attended by Mayor Giuliani. The project was originally scheduled to be completed in August 2003.

In November 2000, unmapped utility and gas lines caught fire, forcing Con Ed to shut down construction and remap the area. Construction workers also discovered an undocumented structure belonging to New York Transit.

The main foundation contractor, meanwhile, Pile Foundation Construction Company, experienced months of delay, after a key portion of the foundation leaked concrete. PFCC had engineers redesign another portion of the foundation at least three times.

In one report, the project manager, Tishman Construction Corporation, referred to Whitehall as “the Little Dig,” in reference to the famously over-budget and behind-schedule tunnel project in Boston that recently sprang leaks.

Since contractors began work on Whitehall, the price tag has risen 41%, to nearly $189 million from $134 million, bringing the combined overage for the two ferry terminals to $86 million – roughly the original projected cost of the terminal on the Staten Island side.

Due to the delays and extra work on the Whitehall terminal, the fee paid to Tishman for construction management has risen more than 50 percent, to $12.8 million from $8 million, and PFCC’s contract increased $3 million.

The delays and inflated costs at the two terminals come at a time when transportation funds are needed in the city. Almost half of New York City roads are in poor condition. Ferry service to Staten Island, used by 60,000 riders a day, has failed to keep up with the needs of the borough’s growing population. And the Metropolitan Transportation Authority is in the midst of an acute budget crisis and is expected to announce fare hikes on the city’s subways and buses and suburban trains and bus lines next week.

The MTA – which shares oversight of the project with the city’s Economic Development Corporation, Department of Parks and Recreation, and Department of Transportation, among other agencies – contributed significantly to the delays and cost overruns on the Whitehall project, according to budget documents. The MTA refused to provide inspectors during the foundation work for more than one six-hour shift a day, placed restrictions on rush-hour work, and moved slowly in approving permits and design changes requested by contractors, according to project documents. An MTA spokeswoman referred questions to New York City Transit, which did not return calls seeking comment.

Officials from the New York City Economic Development Corporation said the delays at Whitehall were unavoidable, given the complexity of the project and the city’s decision to keep the terminal open to commuters throughout construction.

“You need to step back and look into the project in the 1990s,” the president of the city-owned Economic Development Corporation, Andrew Alper, said in a telephone interview last week. “There was a lot of enthusiasm, and the original project schedule was very aggressive. But this is probably the most complex engineering project in the city right now. We’re working very close to subway tunnels, the Battery Park underpass, and utility lines. It’s a very old structure, and like any old building, you find surprises.”

PFCC won the foundation job with a low-bid plan that promised millions in savings. Speaking on the condition that his name would not be used, an executive of one company that bid for the foundation contract in early 2000 said he had been surprised at the low estimate. By the time PFCC finished, its costs had risen by $3 million, with at least three redesigns and emergency change orders that set the project back months and cost the city millions in additional fees for the time of other contractors.

In the end, the project managers declined to solicit a bid from PFCC for additional work on the site, due to “their poor performance,” in the words of a report by the Federal Transit Administration, which provided some of the money for the project and has an oversight role.

PFCC did not return repeated phone calls seeking comment. But in at least one report, executives of the company blame project designers for the general contractor’s problems.

To anchor the approximately 200,000-square-foot building, PFCC installed piles and triple-sleeved caissons, which would channel the load of the three-story structure straight into the ground. After months of construction, however, the company discovered that the caissons had inexplicably leaked cement, potentially skewing the load sideways and threatening the foundation’s structural integrity. In addition, EDC project memos detail numerous “deficiencies” in another portion of the foundation design, requiring repeated redesigns.

Most private developers include clauses in their contracts that reward contractors for finishing early and fine them for finishing late. With millions of dollars in interest payments hanging in the balance, they cannot afford to do otherwise.

PFCC’s contract does have a clause allowing the city to fine the company $500 a day if it does not finish on time. But none of those penalties have been applied. Instead, the EDC agreed to pay PFCC $440,000 to clean out the leaked concrete and at least $500,000 for the numerous redesigns on the caissons and other portions of the foundation.

The steel work was not supposed to start until after the foundation was completed. But project managers had fallen so far behind that they adopted an accelerated schedule, allowing the steel contractor and PFCC to work simultaneously. Afterward, PFCC submitted a change order for $1.78 million, citing “hardships and loss of productivity after the steel was erected.” The charges included costs for idle equipment and loss of productivity. The EDC negotiated the settlement down to about $1.07 million, in credits and new fees.

EDC officials said PFCC was not to blame. Asked about the leaked concrete, one EDC official said she did not know for sure but speculated that the rock on which the caissons were placed was cracked.

EDC officials also downplayed the significance of PFCC’s redesigns for a trapezoidal beam grid, which among other things did not take into account the TA duct bank and the holes for utility lines that were discovered four years ago.

Independent engineers said so many changes are unusual on a project.

“When you get redesigns, subsequent redesigns, and redesigns of redesigns, it sounds like somebody didn’t do their homework,” a director of the Structural Engineers Association, Stephen DeSimone, said. He is president of DeSimone Consulting.

EDC officials disagreed.

“No one was at fault, these were unforeseen field conditions, and neither the designer nor the contractor would have known of the conditions beforehand,” the corporation’s spokesman, Michael Sherman, said. EDC officials said they did not solicit a bid for additional work from PFCC because “there were times when Pile Foundation did not adequately staff the project.” One EDC official, speaking on condition of anonymity, suggested the firm was diverting workers to another city agency’s project.

Both Con Ed and the New York City Transit provided maps of their underground facilities in the area. But on November 3, 2000, shortly after groundbreaking, on Ed gas and electric wires caught fire within the project limits, damaging equipment and forcing a work shutdown while Con Ed remapped the entire area.

“We know where our electrical wires are,” a spokesman for Con Ed, Joe Petta, said. “But occasionally reference points may change. The sidewalk may be widened or narrowed. In any city project we go in and dig test pits to make sure things are where they are supposed to be.”

Officials of New York City Transit and its parent organization, the MTA, did not respond to questions about the unmapped structures on the site. City officials have previously attributed delays to two cold winters, unspecified “unforeseen” work field conditions, and the September 11, 2001, attacks, only blocks from the site.

The Economic Development Corporation’s Mr. Alper said last week that the Whitehall work should be completed by spring. He has also been quoted as saying that the scheduled completion date of the project to expand and rebuild the ferry terminal at St. George on Staten Island has slipped another three months, to next March.