NEW YORK (AP) – High-rise fires are always treacherous, but firefighters who responded to an abandoned ground zero skyscraper faced a series of unforeseen complications in the blaze that killed two of their brethren.

The main water supply failed, the fire was difficult to reach and the condemned 41-story building was thought to pose health risks to emergency responders and the neighborhood.

The former Deutsche Bank office building has been a toxic site since it was damaged on the morning of the 2001 World Trade Center attack, and it was being disassembled.

The cause of the fire was under investigation. Officials said that it was not believed to be electrical and that demolition crews had not been working with torches on Saturday. Fire marshals could not even enter the building until Sunday because small pockets of fire were still burning, but they had been questioning witnesses, including an elevator operator who first reported the blaze.

Investigators also were interested in graffiti inside a work shed that made reference to a burning building, authorities said.

Fire Department of New York spokesman Frank Gribbon said the fire has not been deemed suspicious; authorities have not ruled out every accidental cause.

After the fire was discovered on the 17th floor Saturday afternoon, just steps from the site where 343 firefighters died nearly six years ago, the hundreds of emergency workers who responded encountered immediate difficulties.

The blaze began about a dozen floors up and burned on multiple floors at the building. The water supply system known as the standpipe did not work, forcing firefighters to use ropes to pull hoses to the upper floors to put out the seven-alarm blaze.

“The standpipe was not operating. We don’t know why yet,” Mr. Gribbon said.

The plan for dismantling the building, submitted by the project’s main contractor to the owners last year, included a note that a “dry” standpipe would be maintained throughout the duration of the project.

Dry standpipes do not have water immediately available and can take several minutes to begin flowing, fire science expert Glenn Corbett said. They are typically used in open structures like free-standing parking garages, but city fire and building codes also allow them at demolition projects of this type, he said.

Many other jurisdictions throughout the country would not allow dry standpipes, he said. In some cases, if not capped properly, he said, they can fail and have air pressure problems.

“A dry system is really susceptible to problems,” he said.

A spokeswoman for the main contractor, Bovis Lend Lease, declined comment on the standpipe. The city could not say on Sunday who was responsible for inspecting it.

In addition to the water failure, authorities said some of the materials being used to protect the environment from toxins may have worsened the situation as firefighters tried to control the flames.

More than 10 floors of the skyscraper were sealed off with polyurethane to keep toxic dust containing asbestos, lead and trade center materials from leaking out into the air.

Governor Spitzer of New York said the protective materials were there because of federal Environmental Protection Agency requirements; a spokeswoman for the agency said it was a state labor requirement.

“It is standard operating procedure to put up these kinds of barriers when you’re doing an asbestos abatement job,” EPA spokeswoman Bonnie Bellow said.

No matter what the reason or whose rules were set, Spitzer said the polyurethane sheets on the building “may in fact have made this fire harder to fight.”

“The smoke was being contained and they couldn’t see. They were perhaps disoriented,” he said of the firefighters who died.

The fallen firefighters, Robert Beddia and Joseph Graffagnino, became trapped on the 14th floor, inhaled smoke and died of cardiac arrest. Others broke windows from the inside to get air, authorities said. More than 50 firefighters suffered minor injuries, the department said.

There was also a great deal of plywood and other combustible materials in the building, and firefighters inside were forced to navigate a maze of debris, authorities said. The only ways up were a construction elevator on the outside of the building and stairs inside.

The latest disaster at ground zero invoked memories of the attack nearly six years ago and renewed some of the same concerns that residents in lower Manhattan have had about possible harmful effects of the air.

Several floors of the building, including the one where the fire started, had not been thoroughly cleaned of asbestos and other toxic dust, state officials said. The floor-by-floor dismantling of the building had reduced the tower to 26 stories this week.

Officials said air-quality tests in the neighborhood for asbestos and other contaminants were negative. City environmental officials said 57 air samples near the building tested negative for asbestos since the fire.

Two years ago, redevelopment officials said the building contained excessive levels of seven hazardous substances, including dioxin and lead. As part of the tear-down, a dozen air-quality monitors were installed in the area around the building.

Some scientific studies have indicated that as many as 400,000 people were exposed to toxic ground zero dust. Hundreds have fallen ill, several have died from lung ailments blamed on inhaled trade center ash, and thousands have sued various government entities.

Independent government reviews have faulted the federal EPA’s handling of the immediate aftermath of the attacks, as well as the agency’s cleanup program for nearby buildings.

The tower at 130 Liberty St. has become a persistent headache for redevelopers since the attacks. The 1.4 million-square-foot office tower was contaminated after the trade center’s south tower collapsed into it, raining down toxic dust, debris and human remains.

A series of squabbles over payments, labor and accidents like the steam pipe that fell through a firehouse roof in May have delayed the dismantling of the building, where developers plan to build one of five towers to replace the destroyed World Trade Center.

State officials had been removing a floor a week and had pledged to take the building by the end of the year, but Mr. Spitzer said “it is hard to predict now” when the building would be finished.

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Associated Press writer Amy Westfeldt contributed to this story.