The warnings were issued in a series of pointed letters and closed-door meetings by the Braintree firm of Gannett Fleming from September to December 1999, according to the documents.

The leak, which has yet to be permanently fixed, is expected to delay the opening of the Massachusetts Turnpike connection to the Ted Williams Tunnel by at least three months to December 2003 and will cost up to $10 million to repair. Project officials estimate it could cost another $50 million to $60 million because neighboring contracts will also be delayed.

According to internal letters and meeting minutes obtained by the Globe, at least the outlines of the problem were foretold in 1999, weeks before a giant concrete tunnel box was placed on the floor of the channel.

At that point, Gannett Fleming was blunt in its criticisms of the changes in construction methods, which were proposed by Modern Continental Co., a contractor that has had more Big Dig work than any other company.

A Gannett Fleming engineer wrote to Bechtel/Parsons, the Big Dig's private management consultant, that he had "strong reservations" about the proposed manner of building a watertight closure along the bottom of a huge concrete tunnel box.

He said the method of pouring the concrete slab beneath the tunnel was "problematic." At one point, he described a last-minute construction change in the tunnel as "radically different from the Contract Drawings and Specifications."

That engineer, Donald Nicholas, declined comment yesterday when he was reached in his office. "We're not at liberty to say anything to the press," he said. Modern Continental also declined comment.

Big Dig officials yesterday described the letters as "very important" but only part of the story, and said they had not yet determined the exact cause of the huge leak, and thus have not assessed blame. They have hired the consultant Deloitte & Touche to resolve the complex matter of who should be financially responsible for the leak.

"The important thing is to get the situation stabilized, and there will be ample time to assess culpability," said Michael Lewis, the Big Dig project director.

Six tunnel boxes as big as battleships

"You have to ask, would the same things have happened with the Gannett Fleming designs?" Lewis asked. "They could have happened in any other design as well. That's what has to be investigated."

The work in question is on the Fort Point Channel crossing, which involved building, floating, and placing six battleship-sized concrete tunnel boxes.

The bid on the Fort Point Channel crossing contract in 1997 was $301 million. Even without the cost of repairing the leak, it has now increased to $385 million. Work began in March 1997 and was supposed to be completed by this month. But construction delays, including the recent leak, have put that off until at least late next year.

The problem area involves the westernmost end of the tunnel that will carry eastbound traffic.

Gannett Fleming is the firm that designed the "closures" on both ends of the tunnels, which would keep channel flows out of areas where construction needed to take place.

However, according to the documents and to project officials interviewed yesterday, Modern Continental altered the planned method of constructing an underwater concrete slab on the west side. That slab today is the site of the leaks that have delayed construction.

"The contractor changed the concept," said Michael Bertoulin, who manages construction on the Interstate 90 portion of the Big Dig for Bechtel/Parsons. "We agreed to it." Project officials would not say why it was changed, but contractors often alter methods to save money or time.

Gannett Fleming in September 1999 warned Bechtel/Parsons Brinckerhoff not to change the plans for constructing the slab, because the contractor would no longer be responsible if leaks occurred.

Through November of that year, Gannett Fleming, Modern Continental, and Bechtel/Parsons engineers continued to meet and exchange letters over how to complete the work.

In a Nov. 5, 1999, letter to Bechtel/Parsons, Nicholas said he had "highlighted the issues of seepage and potential blowout of the closure bottom."

By blowout, Nicholas meant a major rupture in the tunnel substructure allowing water to flow into work areas.

In a Nov. 11 letter, Nicholas stated that Modern Continental and other contractors "have dramatically/drastically changed the contract documents for the West Closure Bottom Cut-off System." Again, he said he had concerns about "a new water seepage path underneath" the concrete slab.

Nicholas expressed "strong reservations about the adequacy" of the construction methods Modern Continental was planning.

On Dec. 11, Nicholas said that "what is being discussed is radically different from the Contract Drawings and Specifications" and warned Bechtel/Parsons of "ramifications of acceptance of the change."

Those ramifications became clear, as feared, in early July when, because of continuous leakage, water could not be drained from an area on the west side of the channel where about 180 feet of underground roadway needed to be built.

Drilling dozens of holes in a 40-foot-thick floor

Several weeks ago, engineers took the drastic step of drilling 80 holes through the 40-foot-thick floor of their tunnel box near the leak site and injecting thousands of pounds of cement and chemical grout into the area below to try to stem the flow.

"This should be considered as a last resort," Nicholas told the project director in a letter only six weeks ago. "It is difficult for Gannett Fleming Inc. to help solve the problem . . . since our closure details were not followed by the contractor, and we do not know what was actually constructed."

Project officials said last week that the leak appears to have stopped. But, to be sure, they have begun building an underground concrete sealer wall along the base of the 168-foot-wide face of the tunnel. That wall, they said, would stop any further leaks that might occur as pressure builds with the rising tide.

The tunnel leak comes as project officials acknowledged last summer that they had a serious problem with the strength of a huge beam on the new Leonard P. Zakim/Bunker Hill Bridge. A Swiss bridge engineer brought the issue to the project's attention almost two years earlier, but engineers said they were unable to confirm the problem's existence until last May.

The contractor is now repairing the beam, at an estimated cost of $300,000.