David Reese, 53, of Gilboa, N.Y., 50 miles southwest of Albany, was charged with second-degree murder in the death of Aron J. Thomas, 33, of Olivebridge, N.Y., near Kingston, where the shooting occurred, Ulster County District Attorney Holley Carnright told reporters.
Police said they found Thomas dead of a gunshot wound in the Kingston office of the New York City Department of Environmental Protection at 6:46 a.m.
Kingston is about 90 miles north of New York City.
There were no other injuries in the shooting, Carnright said.
Reese didn't put up any resistance when he was arrested, Kingston Police Chief Egidio Tinti told the Times Herald-Record of Middletown, N.Y.
He pleaded not guilty during an arraignment in Kingston City Court and was sent to the Ulster County Jail without bail.
A decision was to be made Tuesday about whether he was eligible for counsel by a public defender.
Leaving the court in shackles and an orange jumpsuit that was too small for him, Reese told the Record, "I'm innocent" and then chuckled, the Record said.
The DEP office, in midtown Kingston a block from a major thoroughfare, employs 100 to 150 people who work in the department's reservoir water-quality laboratory and other offices overseeing the city's upstate reservoirs. Some DEP police are also stationed at the facility.
Authorities gave no motive for the killing. But the Record said the apparent motive was a dispute between the two men, who both worked in the same area of the building.
The newspaper gave no further details.
Reese worked as a mechanical and electrical technician. Thomas was a watershed maintainer, responsible for facilities upkeep, DEP spokesman Adam Bosch said.
The building was closed after the shooting.
Employees, hugging each other outside the building, declined to comment about what happened, the Record said.