"There is nothing concrete to suggest this plot ever went beyond the aspirational or talking stage," said a U.S. official familiar with the intelligence that led to the warning.
Law enforcement officials told ABCNews.com the information was based on an FBI source who has proved "reliable and knowledgeable in the past."
Officials told ABCNews.com unspecified new information in the last 48 hours led to the public warning "out of an abundance of caution."
Congressman Peter King (R-NY), the top Republican on the House Homeland Security Committee, told the Associated Press "authorities have very real specifics as to who it is and where the conversation took place and who conducted it."
The FBI's source reportedly told agents of an al Qaeda-connected group's desire to place bombs or suicide bombers inside the first and last Long Island Rail Road commuter cars and detonate them as the train entered Pennsylvania Station in Manhattan, also used by the Washington-New York-Boston Amtrak system and the New York City subway.
Senior FBI officials said their source said the group began its discussions "in late September."
The officials confirmed the nature of the plot and said that FBI agents worked through the night Monday to shape the language of a memo sent to local law enforcement.
"Transit passengers in larger metropolitan areas like New York may see an increased security presence in the coming days. This includes uniformed and plain clothed behavior detection officers, federal air marshals, canine teams, and security inspectors," said Russ Knocke, a Department of Homeland Security Spokesman. He said there were no plans to raise the current threat level.
New York City Deputy Police Commissioner for Public Information Paul Browne said in a statement: "The New York City Police Department is aware of an unsubstantiated report indicating that Al Qaeda terrorists discussed targeting mass transit in New York City and vicinity. We have no information indicating that these discussions advanced beyond the aspirational stage, but in an abundance of caution, the NYPD has deployed additional resources in the mass transit system. It is not uncommon for the department to receive threat information and to adjust our resources accordingly."
FBI and New York counter-terrorism officials involved in assessing the threat said they hardly viewed the warning as a "routine matter."
"We are coordinating and communicating with the region's transit and security agencies to provide seamless operations during this exceptionally busy time," said Michael Balboni, the NY State Deputy Secretary for Public Safety. "This is a continuation of ongoing operations that have been in place for some time, with different patrolling mechanisms to ensure the safety of mass transit."
The FBI warning was made public on the morning of the busiest travel day in the country. Many New York commuters leave their city jobs early on Thanksgiving eve.