"This afternoon, I called the White House and told them I thought it would be a very good idea that they look for alternative sites," said Sen. Chuck Schumer, D-N.Y.
Chair of the Senate Intelligence Committee Sen. Dianne Feinstein, D-Calif., sent a letter to Obama today urging him to reconsider holding the trials in New York City. She cited the Christmas day bombing attempt.
"The terrorist threat to the United States remains high," she wrote. "Without getting into classified details, I believe we should view the attempted Christmas Day plot as a continuation, not an end, of plots to strike the United States by al Qaeda and its affiliates."
When the plan to try the terror suspects in New York City was first announced in November, it was met with a lukewarm response.
The Obama administration had put a lot of weight behind the symbolism of trying the suspects at the scene of the crime.
One line of thinking behind trying the suspected terrorists in federal court -- rather than using military commissions -- was that it would send a powerful message to the international community and undo some of the damage the Guantanamo Bay detention camp has done to the U.S. image abroad.
The primary message would be that the United States can use its traditional federal courts to try, convict and execute the people who devised the deadliest terrorist attack ever on U.S. soil, and New York was the "sentimental favorite," as one source said.
New York City officials projected that it would cost $400 million to provide security if the trial of the Sept. 11 suspects took two years. The mayor's office estimated that it would cost another $206 million annually if the trial ran beyond two years, which some say is possible.
Six senators from both parties wrote a letter to Attorney General Eric Holder Tuesday urging him to abandon the idea.
Rep. Peter King, R-N.Y., said Thursday he has introduced a bill that would prohibit the use of Justice Department funds to try Guantanamo detainees in federal civilian courts.
Local officials echoed similar concerns.
"Every time there is a loud noise during the two years of those trials, it's going to frighten people and I think New Yorkers have been through enough," Gov. Paterson said.
The five suspects are Mohammed, Walid Muhammad Salih Mubarek Bin 'Attash, Ramzi Binalshibh, Ali Abdul Aziz Ali and Mustafa Ahmed Adam al Hawsawi.
ABC News' Jake Tapper and the Associated Press contributed to this report.