Monitoring stations now used to check air pollution will be fitted with filters to detect biological agents, officials from the Environmental Protection Agency said.
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We're still on guard here in America
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President George W Bush
A network of laboratories will analyse results which raise concern and come up with answers within 24 hours, they said.
The system will be co-ordinated by the Homeland Security Department, which comes into being on Friday.
White House spokesman Ari Fleischer said: "It's part of our precautions to protect the country."
He and other officials said they knew of no imminent danger.
Five people died after anthrax spores were sent to politicians and news organisations just weeks after the 11 September attacks in 2001.
No-one has been charged with the anthrax attacks.
The US Senate confirmed Tom Ridge as the first secretary of Homeland Security on Wednesday.
Vaccinations
Fears have also been raised of smallpox being used as a weapon.
President George W Bush ordered all military personnel to be vaccinated ahead of a possible conflict in the Gulf.
He had the inoculation himself and it is being made available to members of the public concerned about an attack.
Mr Bush again acknowledged people's fears of "gathering dangers" from outside the US as officials gave details of the new system.
"We're still on guard here in America," he said.
Olympic trial
Many of the 4,000 existing environmental monitoring stations are being converted immediately, EPA spokesman Joe Martyak said.
The system using filters to detect large amounts of potentially dangerous airborne pathogens was tested throughout 2002, including at the Winter Olympics in Salt Lake City.
The sooner health officials detect a bio-terrorism attack - such as the release of germs from a plane - the sooner they can treat anyone already infected and protect others.
The filters will be checked for biological agents by the federal Centers for Disease Control and Prevention's Laboratory Response Network.
These tests are considered much more reliable than handheld devices used by emergency responders, which often indicate the presence of a particular germ when none is there.