They say that some of them are likely the cause of the current outbreak, which has led to 46 cases, and 22 hospitalizations, so far.
The city said that Department of Health officials will release a list of addresses of other locations in the coming days.
"It's not very comforting to know that there's something nearby that can be dangerous," said Upper East Side resident Stephen Gainsburg.
Near Gainsburg's home, Eyewitness News spotted a team of water treatment specialists working at a building at 1511 Third Ave., which the city is calling "a cooling tower of interest."
Testing began July 2 after officials identified an outbreak of Legionnaires' disease in three ZIP codes on the Upper East Side.
The Health Department told Eyewitness News that the initial PCR test at a commercial building at the corner of East 85th Street came back positive for Legionella bacteria. They added that it's unclear whether it's active or an environmental contaminant.
"I use Equinox, so that could be a little bit of a problem. I was there the other day," said Upper East Side resident Jerry Wallach.
The Health Department ordered the building owner to immediately remediate, drain, clean and disinfect the cooling tower.
The team working at the building said they are doing just that, along with carrying out a new mandatory monthly testing.
That requirement is something that Eyewitness News first reported about in May at a cooling tower in East Harlem that was part of another outbreak last summer.
During that outbreak, seven people died, and more than 100 got sick with Legionnaires' disease.
The bacteria are spread by mist from cooling towers and by water droplets outside. Experts stress that it's not inside buildings.
"They should publish the addresses - are they going to?" said Upper East Side resident Dorothy Wallach.
Mayor Zohran Mamdani vowed to be transparent, but the list of the "cooling towers of interest" in the affected area has not yet been released.
Testing is nearly complete, but some critics say it's taking too long.
"What are we waiting for? Are we going to wait for more people to get sick and potentially die?" said New York City Councilmember Julie Menin.
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