ROCHESTER — The Lake Shore Limited runs between Chicago and New York City without crossing the Canadian border. But when it stops at Amtrak stations in western New York State, armed Border Patrol agents routinely board the train, question passengers about their citizenship and take away noncitizens who cannot produce satisfactory immigration papers.

“Are you a U.S. citizen?” agents asked one recent morning, moving through a Rochester-bound train full of dozing passengers at a station outside Buffalo. “What country were you born in?”

When the answer came back, “the U.S.,” they moved on. But Ruth Fernandez, 60, a naturalized citizen born in Ecuador, was asked for identification. And though she was only traveling home to New York City from her sister’s in Ohio, she had made sure to carry her American passport. On earlier trips, she said, agents had photographed her, and taken away a nervous Hispanic man.

He was one of hundreds of passengers taken to detention each year from domestic trains and buses along the nation’s northern border. The little-publicized transportation checks are the result of the Border Patrol’s growth since 9/11, fueled by Congressional antiterrorism spending and an expanding definition of border jurisdiction. In the Rochester area, where the border is miles away in the middle of Lake Ontario, the patrol arrested 2,788 passengers from October 2005 through last September.

The checks are “a vital component to our overall border security efforts” to prevent terrorism and illegal entry, said Rafael Lemaitre, a spokesman for United States Customs and Border Protection. He said that the patrol had jurisdiction to enforce immigration laws within 100 miles of the border, and that one mission was preventing smugglers and human traffickers from exploiting inland transit hubs.

The patrol says that answering agents’ questions is voluntary, part of a “consensual and nonintrusive conversation” Some passengers agree, though they are not told that they can keep silent. But others, from immigration lawyers and university officials to American-born travelers startled by an agent’s flashlight in their eyes, say the practice is coercive, unconstitutional and tainted by racial profiling.

The Lake Shore Limited route is a journey across the spectrum of public attitudes toward illegal immigrants — from cities where they have been accepted and often treated as future citizens, to places where they are seen as lawbreakers the federal government is doing too little to expel.

The journey also highlights conflicting enforcement policies. Immigration authorities, vowing to concentrate resources on deporting immigrants with serious criminal convictions, have recently been halting the deportation of students who were brought to the country as children without papers — a group the Obama administration favors for legalization.

But some of the same kinds of students are being jailed by the patrol, like a Taiwan-born Ph.D. candidate who had excelled in New York City public schools since age 11. Two days after he gave a paper on Chaucer at a conference in Chicago last year, he was taken from his train seat and strip-searched at a detention center in Batavia, N.Y., facing deportation for an expired visa.

For some, the patrol’s practices evoke the same fears as a new immigration law in Arizona — that anyone, anytime, can be interrogated without cause.

The federal government is authorized to do just that at places where people enter and leave the country, and at a “reasonable distance” from the border. But as the patrol expands and tries to raise falling arrest numbers, critics say, the concept of the border is becoming more fluid, eroding Constitutional limits on search and seizure. And unlike Arizona’s law, the change is happening without public debate.

“It’s turned into a police state on the northern border,” said Cary M. Jensen, director of international services for the University of Rochester, whose foreign students, scholars and parents have been questioned and jailed, often because the patrol did not recognize their legal status. “It’s essentially become an internal document check.”

Domestic transportation checks are not mentioned in a report on the northern border strategy that Customs and Border Protection delivered last year to Congress, which has more than doubled the patrol since 2006, to 2,212 agents, with plans to double it again soon. The data available suggests that such stops account for as many as half the reported 6,000 arrests a year.

In Rochester, the Border Patrol station opened in 2004, with four agents to screen passengers of a new ferry from Toronto. The ferry went bankrupt, but the unit has since grown tenfold; its agents have one of the highest arrest rates on the northern border — 1,040 people in the 2008 fiscal year, 95 percent of them from buses and trains — though officials say numbers have fallen as word of the patrols reached immigrant communities.