US homeland security chief Tom Ridge says it was essential to raise security alerts in some cities after analysing information on possible al-Qaeda plans.
Security has been stepped up in New York and other cities
Mr Ridge said security had made it more difficult for terrorists, but vowed: "We will not become Fortress America."
Warnings were issued on Sunday from what was said to be "new" information, though officials now say al-Qaeda gathered it up to four years ago.
But some of it may have been updated as recently as January of this year.
Meanwhile officials in Pakistan denied suggesting that information gathered following the arrest of an al-Qaeda suspect contained plans for fresh attacks in the US or Britain as had been reported.
But the Pakistani information minister said the recent arrests of suspects were clear evidence that the security forces had finally penetrated al-Qaeda networks in Pakistan.
Arrests have also been made in the UK. Police said 13 men of Asian origin had been detained as part of inquiries into alleged international terrorism.
Mr Ridge rejected partisan criticism that the timing of the latest warning was designed to knock John Kerry out of the headlines following his nomination as the Democratic Party's presidential candidate last week.
"We do not do politics at the Department of Homeland Security," Mr Ridge said. "Our job is to
identify the threat."
BBC diplomatic correspondent Jonathan Marcus says some leading Democrats believe that the Bush administration is playing the terrorism card for all it is worth.
But he adds that whatever lies behind this heightened alert, the broader threat remains real enough and is likely to grow as November's election gets closer.
Officials confirmed on Tuesday that some of the information used to identify specific threats in New York, Washington DC, and Newark, New Jersey, dated back to 2000 and 2001 - before the 11 September 2001 attacks.
But the detail in the information, coupled with intelligence that al-Qaeda may be planning a new attack on the US before the presidential election, justified making it public, Mr Ridge said.
"I would point out that [these are] the most significant detailed pieces of information about any particular regions that we have come across in a long, long time, perhaps ever and that is why we decided to share it publicly."
Reports in leading US newspapers say officials were unsure if Osama Bin Laden's network was still conducting surveillance on the sites named as potential targets.
Homeland security adviser Frances Townsend confirmed: "You can't tell from the intelligence
itself whether or not those individuals [who amassed it]
are still here."
Raids in Pakistan reportedly turned up hundreds of photos, sketches and written documents, which included details on the number of pedestrians passing named buildings, and whether explosives would be able to melt the steel holding them up.
A computer and communications expert reportedly linked to al-Qaeda, Mohammad Naeem Noor Khan, and one of the US' most wanted terror suspects, Ahmed Khalfan Ghailani, were among those held by the security forces.
Pakistani officials also say that security forces have arrested eight more people in the last two days.
Their identities have not been disclosed, but officials said more arrests were expected in the next few days.
Mr Ridge praised employees at the buildings named as possible targets: the New York Stock Exchange, the Citigroup Center building in New York, the International Monetary Fund and World Bank buildings in Washington DC, and Prudential Financial's headquarters in Newark, New Jersey.
"Just by showing up to work you have made a powerful statement that they [terrorists] will not succeed," he said.