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(The following article by Eric Lipton was posted on the New York Times website on July 14.)

WASHINGTON — The Senate struggled Thursday to settle upon an appropriate response to last week’s bombings in London after an emotional debate broke out over how best to allocate antiterrorism spending between mass transit and other security needs.

In three votes, the Senate, unable to reach a consensus on how much to spend, rejected proposals to increase the Homeland Security Department’s budget for mass transit and rail by amounts ranging from $100 million to $1.4 billion.

It finally voted 96 to 1 to adopt a $31.9 billion spending plan for Homeland Security in the 2006 fiscal year that appropriates $100 million for transit security, which is $50 million less than in this year’s budget.

The measures to increase transit security spending failed even though a majority of the Senate voted in favor of one plan – a $1.16 billion expansion in rail and transit grants proposed by Senator Richard C. Shelby, Republican of Alabama.

The vote, 53 to 45, was insufficient for passage under Senate rules because the amendment would have exceeded an agreed budget cap for the department, requiring that it pass by a three-fifths vote.

“I am the first to admit this is a large sum and we must balance our spending on public transportation with other priorities,” Mr. Shelby said. “But we must guard against what the world witnessed last week in London.”

The debate unfolded after Homeland Security Secretary Michael Chertoff made remarks to reporters over the last two days defending the heavy emphasis in federal antiterrorism spending on protecting aviation and addressing other threats, rather than providing security for mass transit.

Over the last four years, Homeland Security has allotted $250 million to transit security grants, compared with about $15 billion for aviation security.

“The truth of the matter is, a fully loaded airplane with jet fuel, a commercial airliner, has the capacity to kill 3,000 people,” Mr. Chertoff said in an interview Thursday with The Associated Press. “A bomb in a subway car may kill 30 people. When you start to think about your priorities, you’re going to think about making sure you don’t have a catastrophic thing first. But it doesn’t mean that we only focus on aviation. We do aviation, we do other things as well, but we scale our response based on the nature of the architecture.”

The comments reflected the general philosophy Mr. Chertoff has adopted since taking over Homeland Security five months ago, as he has repeatedly argued that the nation cannot try to defend equally against every possible strike.

“A nuclear weapon that killed a million people is a different order of consequence than 50,” Mr. Chertoff said Wednesday, in a separate interview with The New York Times.

But Mr. Chertoff’s comments drew an immediate rebuke on Thursday on the Senate floor, where the debate over the Homeland Security budget was already under way.

“When Americans are at risk, Americans are at risk,” said Senator Jon Corzine, Democrat of New Jersey. “I would suggest anybody who wanted to seek large concentrations of people at any one time, I’ll take you to Hoboken train station every workday.”

Senator Charles E. Schumer, Democrat of New York, demanded that Mr. Chertoff apologize, even suggesting that he consider resigning.

“These are some of the most appalling things that I have heard coming from any government official in a long, long time,” Mr. Schumer said in remarks on the Senate floor. “And if this administration is embarked in a new policy, which says that we’ll protect people in the air but not on the rails, and washes their hands of that responsibility, then they ought to let America know. And they’ll be facing the fight of their life on this floor.”

Senator Judd Gregg, Republican of New Hampshire, came to the defense of Mr. Chertoff, saying: “Anybody who has any intellectual honesty about how we pursue terrorism must be ready to say there isn’t enough money in the federal treasury to effectively address securing the entire transit system of America.”

Mr. Gregg, chairman of the committee that handles the Homeland Security budget, said it would be reasonable, after the London bombings, to add $100 million to the spending plan for mass transit security, doubling the proposed budget.

But after one proposal to spent more than $1 billion extra on mass transit and rail was defeated, Democrats and some Republicans joined to defeat the measure, partly because it would be financed by cutting grants to emergency responders. Transit spending could still be increased during negotiations with the House, which had adopted its 2006 fiscal year budget for Homeland Security, calling for $150 million in transit grants.

The debate came on a day when Mr. Chertoff testified at two hearings on his plan to reorganize Homeland Security, which he announced Wednesday. At both, he was asked about rail security.

“We could never run the New York City subway station like we run an airport,” Mr. Chertoff told the House Homeland Security Committee. “We couldn’t have people walk through magnetometers. It’s not possible.”

But at a Senate hearing later in the afternoon, under questioning from Sen. Joseph I. Lieberman, Democrat of Connecticut, Mr. Chertoff said he wanted to clarify his remarks.

“I do want to emphasize, so there is no mistake about it, that as we speak, and before London, we were working very, very hard focusing on the rail system,” Mr. Chertoff said.

On Thursday, Mr. Chertoff also announced the appointment of Jeffrey W. Runge, an emergency medicine physician who serves as administrator of the National Highway Traffic Safety Administration, as Homeland Security’s new chief medical officer.

Mr. Runge will oversee planning for the large numbers of casualties that might occur in a biological or nuclear attack.

The position is one of several Mr. Chertoff is creating – including a chief intelligence officer and policy and operations directors – as he tries to improve management of the 180,000-employee department.

Carl Hulse contributed reporting for this article.