Firefighters worked round the clock at the devastated site
The condition has been dubbed 'World Trade Center cough' by New York City's fire department, the New York Times newspaper reports
One firefighter has been treated for allergic alveolitis, a rare lung inflammation.
And a Wall Street Journal editor who works near Ground Zero developed a life-threatening autoimmune disease from ingesting the dust.
Dr David Prezant, the chief pulmonary physician for the department said it was common for firefighters to have a brief spell of coughing after attending a fire.
'Still suffering'
But he said many of the firefighters who worked around-the-clock at Ground Zero are still suffering symptoms six weeks after the disaster.
They have been given steroid inhalants to treat coughing and heaviness in the chest.
The treatment aims to ease inflammation and reduce the coughs, and is generally given to people with asthma or chronic bronchitis.
Dr Prezant said 370 firefighters have been fully examined and given chest X-rays.
Up to 10,000 check-ups could take place within a month, he said.
Dr Prezant added: ''We know medically that from inhaling large particulate matter, the consequences can range from chronic cough to asthma to a higher incidence of heart attacks.''
Thomas Manley, the health and safety officer for the Uniformed Firefighters Association, said: 'My level of concern is high.
"We do not know what we may have inhaled in the opening stages of the operation.''
Christie Whitman of the Environmental Protection Agency said workers at Ground Zero had to take precautions to protect their health.