Three construction supervisors and a subcontractor were indicted Monday on manslaughter charges in the 2007 deaths of two firefighters at a skyscraper that once housed Deutsche Bank at ground zero.

The charges cap a 16-month investigation that exposed numerous failures by city officials.

The people charged include two senior officials at subcontractor John Galt Corp. and a manager with general contractor Bovis Lend Lease, the Manhattan district attorney's office said. The Galt company also was charged.

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All face charges of manslaughter, criminally negligent homicide and reckless endangerment.

"Everybody who could have screwed up, screwed up here," District Attorney Robert Morgenthau said of the fire.

The city had acknowledged failing to inspect the building for fire hazards but was not charged in the deaths, angering relatives of the dead firefighters.

While the city made major mistakes, governments are generally immune from criminal prosecutions under a centuries-old legal doctrine called "sovereign immunity," Morgenthau said.

Prosecutors did reach an agreement with the city and Bovis Lend Lease that requires them to institute major safety measures.

Mayor Michael Bloomberg said in a statement: "We will now be creating an additional civilian inspection unit at the Fire Department dedicated to construction, demolition and abatement sites."

The investigation concluded that breakdowns by the Fire Department and Department of Buildings "contributed to the conditions that led to the deaths" of the firefighters, prosecutors said.

Lawyers for Galt and two of the officials named in the indictment didn't immediately return messages seeking comment Monday.

Daniel Castleman, Morgenthau's chief deputy, said a second grand jury is investigating issues related to the fire, other than the firefighters' deaths.

Firefighters Robert Beddia and Joseph Graffagnino were found dead of smoke inhalation in the former bank tower, a building heavily damaged in the Sept. 11 attacks. The tragedy demonstrated a series of failures at the project, including no standpipe to supply water to the upper floors.

Joseph Graffagnino Sr., the father of one of the victims, said Monday the results of the probe "wasted a lot of taxpayers' time and a lot of taxpayers' dollars."

"The city seems to go after the little guys. They could have done this from the second day after the fire," Graffagnino said. "Why wait [16] months just to go indict the John Galt Company?"

Galt was a subcontractor hired by Bovis and the building's owner, the Lower Manhattan Development Corp., to remove toxic debris from the building and take it down floor by floor. The 41-story tower had been dismantled to 26 stories before the fire. It remains at that height.

Prosecutors said that it was an extraordinarily complicated investigation. They interviewed more than 150 people, examined more than 3 million documents and presented 80 witnesses to the grand jury. The transcript of the testimony is 6,500 pages long.

The defendants are Jeffrey Melofchik, the site safety manager for Bovis; Mitchel Alvo, director of abatement for John Galt; and Salvatore DePaola, a Galt foreman.

The penalty for second-degree manslaughter is five to 15 years in prison.

A primary focus of the investigation was the numerous hazards at the tower: The pipe supplying water to fire hoses was broken and the sprinklers didn't work, stairwells were blocked with plywood paneling meant to keep toxic debris in, no working elevator existed inside the building, and an air pressure system created more smoke.

A construction worker's carelessly tossed cigarette caused the fire, but investigators had spent much of the time investigating who was responsible for the maze of fire hazards in the building that hampered firefighters' efforts in the tower. They included the cut standpipe, blocked stairwells, thick plastic sheeting to cover toxic debris that trapped smoke in the building and a negative air pressure system that pushed flames down toward the firefighters.

The Fire Department — which had a firehouse next door — acknowledged it hadn't regularly inspected the building, as city law requires, for more than a year. Other city and state regulators had also been in the tower on a near-daily basis, but didn't report the hazards.

Michael Barasch, an attorney for the Beddia family, said Monday news of charges represented "a bittersweet moment" for the family. "They're not surprised at all, in light of the many willful OSHA violations" cited against both Bovis and Galt, he said.

The Occupational Safety and health Administration fined both contractors a combined $464,500 earlier this year for more than 40 safety violations at the building.

Barasch also said the family intended to pursue lawsuits against the contractors and the city.

The former bank building's demolition was put on hold for about a year because of the blaze. The building's removal had been stalled previously by the discovery of hundreds of Sept. 11 victims' body parts left in the building and other accidents, one that sent a pipe through the roof of the neighboring firehouse.