Lt Howard Bischoff and firefighters Robert Leaver and Daniel Heglund died Monday.
Fire Commissioner Daniel Nigro says their deaths are "a painful reminder that 13 years later we continue to pay a terrible price for the department's heroic efforts."
The three worked at the World Trade Centre site after the attacks. One had leukemia, one had esophageal cancer and a third had colon cancer.
The Uniformed Fire Officers Association says first responders showed health problems soon after the attacks, with 99 per cent of exposed firefighters reporting at least one new respiratory illness.