Emergency workers attempted to rescue the workers from the rubble but they were both pronounced dead after being pulled from the trench.
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The airport warned of traffic delays in the area due to the recovery efforts near Terminals 5 and 7, but flights were not impacted.
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The FDNY first received the call about the construction accident at 11:25 a.m.
At the time of the incident, workers were relocating utility lines in the vicinity of a cogeneration plant to support the increased energy needs of the JFK redevelopment project.
Some 12 units with 60 firefighters responded to the scene, but the workers could not be saved.
The Port Authority of New York and New Jersey issued a statement saying that a stop order for all construction at JFK has been issued.
The identities of the victims were not yet known.
The Port Authority said it is conducting a thorough investigation and will cooperate with all other investigative agencies.
Gov. Kathy Hochul released a statement saying that her thoughts are with the loved ones of the two victims.
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