Officials said the warning, based on information obtained from Al Qaeda prisoners in mid-October, suggested that terrorists may try to destroy bridges or key sections of track.
"The group has considered directly targeting U.S. passenger trains, possibly using operatives who have a Western appearance," the FBI said Thursday in a statement that was issued to state and local law enforcement agencies.
Captured Al Qaeda photographs of U.S. railroad engines, cars and crossings raised concern about the threat, the FBI said.
The warning is the second this month. On Oct. 9, the FBI and several federal agencies overseeing high-risk sectors such as transportation, energy and agriculture sent warnings urging extra precautions.
Gordon Johndroe, Homeland Security spokesman, said the agency is coordinating efforts to tighten security with the Department of Transportation and other federal agencies, as well as the private sector, and state and local governments.
"The American people should still ride our nation's rails and know that this warning has been provided to state and local law enforcement, and the appropriate security officials, so they can take the appropriate steps to increase protective measures," Johndroe said.
Amtrak President David Gunn said federal transportation officials told him about the warning.
"The threat, like a lot of others, is not specific," Gunn said.
The passenger railroad is taking steps to enhance security, Gunn said, although he declined to describe them except to say riders won't notice them.
Around the Sept. 11 anniversary, Amtrak announced that it intended to enforce tighter identification requirements, including random ID checks of passengers on trains.
But Amtrak decided to reconsider that plan and has never implemented it.
New York Gov. George Pataki said his office had contacted the Metropolitan Transportation Authority, the port authority and local law enforcement.
"We are vigilant in protecting public services and infrastructure points across this state," Pataki said, adding that there was no specific threat against New York.
Edward R. Hamberger, president of the Assn. of American Railroads, said that in the past year, railroads developed a security plan that includes a round-the-clock operations center linking railroad control centers with law enforcement agencies and increased surveillance.
"The nation's railroads will not be a soft target for terrorists," Hamberger said.
Intelligence officials continue to believe that Al Qaeda plans to attack other symbols of U.S. economic interests, the FBI said.
U.S. intelligence has learned from additional Al Qaeda prisoners that the terrorist group may be planning strikes on oil tankers as part of an attack on the global petroleum industry, the FBI said.
"Such attacks may be a part of more extensive operations against port facilities and other energy-related targets, including oil facilities and nuclear power plants," the FBI said.
Terrorists believed linked to Al Qaeda attacked a French oil tanker off the coast of Yemen earlier this month.