In a note on the paper's Web site Sunday, Executive Editor Bill Keller said the Times spent weeks discussing with Bush administration officials whether to publish the report.
He said part of the government's argument was that the anti-terror program would no longer be effective if it became known, because international bankers would be unwilling to cooperate and terrorists would find other ways to move money.
"We don't know what the banking consortium will do, but we found this argument puzzling," Keller said, pointing out that the banks were under subpoena to provide the information. "The Bush Administration and America itself may be unpopular in Europe these days, but policing the byways of international terror seems to have pretty strong support everywhere."
The note to readers was published the same day Rep. Peter King (news, bio, voting record) urged the Bush administration to prosecute the paper.
"We're at war, and for the Times to release information about secret operations and methods is treasonous," the New York Republican told The Associated Press.
Keller said the administration also argued "in a half-hearted way" that disclosure of the program "would lead terrorists to change tactics."
But Keller wrote that the Treasury Department has "trumpeted ... that the U.S. makes every effort to track international financing of terror. Terror financiers know this, which is why they have already moved as much as they can to cruder methods. But they also continue to use the international banking system, because it is immeasurably more efficient than toting suitcases of cash."
Stories about the money-monitoring program also appeared last week in The Wall Street Journal and Los Angeles Times. But King, who is chairman of the House Homeland Security Committee, said he singled out the New York paper because it also disclosed a secret domestic-wiretapping program in December.
He charged that the paper was "more concerned about a left-wing elitist agenda than it is about the security of the American people."
King said he would write Attorney General Alberto Gonzales, urging that the nation's chief law enforcer "begin an investigation and prosecution of The New York Times — the reporters, the editors and the publisher."
King's action was not endorsed by the chairman of the Senate Judiciary Committee, GOP Sen. Arlen Specter (news, bio, voting record) of Pennsylvania.
"On the basis of the newspaper article, I think it's premature to call for a prosecution of The New York Times, just like I think it's premature to say that the administration is entirely correct," Specter told "Fox News Sunday."
After the Sept. 11 attacks, Treasury officials obtained access to a vast database called Swift — the Society for Worldwide Interbank Financial Telecommunication. The Belgium-based database handles financial message traffic from thousands of financial institutions in more than 200 countries.
Democrats and civil libertarians are questioning whether the program violated privacy rights.
The service, which routes more than 11 million messages each day, mostly captures information on wire transfers and other methods of moving money in and out of the United States, but it does not execute those transfers.
The service generally does not detect private, individual transactions in the United States, such as withdrawals from an ATM or bank deposits. It is aimed mostly at international transfers.
Lucy Dalglish, executive director of the Reporters Committee for Freedom of the Press, said the paper acted responsibly, both in last week's report and in reporting last year about the wiretapping program.
"It's pretty clear to me that in this story and in the story last December that the New York Times did not act recklessly. They try to do whatever they can to take into account whatever security concerns the government has and they try to behave responsibly," Dalglish said. "I think in years to come that this is a story American citizens are going to be glad they had, however this plays out."
In recent months, journalists have been called into court to testify as part of investigations into leaks, including the unauthorized disclosure of a CIA operative's name.
Gonzales has said the First Amendment right of a free press should not be absolute when it comes to national security.
Interesting Americans are now wondering if the First Amendment should be scaled back a bit. So with such a lose of civil liberties what are Americans fighting for again??