The lawsuit filed in U.S. District Court in Manhattan accused the agency of making misleading statements about air quality after the Sept. 11, 2001, terrorist attacks.
The lawsuit, which seeks class-action status, said the EPA left people "unnecessarily exposed to potentially hazardous levels of asbestos and possibly other carcinogens and toxic substances."
It accused the agency and its leaders, including former EPA Administrator Christie Whitman, of "a shockingly deliberate indifference to human health."
The lawsuit seeks unspecified damages and reimbursement for cleanup and asks the court to order a fund be set up to finance medical monitoring for conditions resulting from exposure to trade center dust.
The agency, in a statement, said it had not seen the lawsuit and could not comment directly on it, but defended its staff's "remarkable feats" after the attacks - including the monitoring and sampling of air, dust, and river and drinking water.
The EPA also said it provided thousands of respirators for response workers, conducted studies of indoor cleaning methods, and cleaned and tested thousands of homes in lower Manhattan.