The federal government has rejected a request by the MBTA and other big-city transit agencies to use antiterrorism grants to install systems that detect chemical threats in subway stations.

The MBTA has had the technology in one of its stations since 2001, as part of a pilot project, and acting MBTA Police Chief Paul S. MacMillan wants to use an estimated $3 million from this year's Homeland Security grant to outfit three more stations. But federal guidelines now exclude the systems under the belief that they would not warn passengers quickly enough.

"We think it's another level of protection that we could use in our subway system to prevent a terrorism attack," MacMillan said.

MacMillan said the system acts like an air filter and sets off an alarm, warning passengers to leave the station if it detects a dangerous chemical. He said the pilot sensor installed earlier this decade has worked in tests; it is also occasionally set off by cleaning chemicals used to scrub down the station, he said. MacMillan would not say which station has the detectors, or which stations he wants to add, citing security concerns.

There is disagreement, however, about how effective such systems would be in the event of a real emergency, something the T has not faced. Companies that produce the equipment have been actively lobbying to make the technology eligible to be covered by the grant.

The Transportation Security Administration, which administers the grants for the Department of Homeland Security, has declined to pay for the systems, sought by most major transit agencies. It has instead focused its grant program on training, surveillance, public awareness, and making stations and tunnels more physically resistant to explosive attacks.

"Current chemical detection systems do not warn the traveling public or system operators in a real-time environment that would deter or prevent a catastrophic event or attack," said Christopher White, a TSA spokesman. "We're very focused on active items, funding active activities and projects that would deter a terrorist attack."

Michael Strano, an MIT chemical engineer who studies technologies for detecting chemical and biological agents, said the current technology is not completely adequate against all biological and chemical threats.