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An Amtrak/VIA train from New York to Toronto passes through Oakville April 22, 2013For the Globe and Mai

A man arrested in New York in connection with an alleged terror plot to attack Via Rail did not enter the United States through Canada, the Harper government says.

Immigration Minister Jason Kenney made this known Friday to beat back suggestions in the United States that Ahmed Abassi had arrived there via Canada – a sensitive topic for Ottawa because American politicians and commentators regularly paint their northern neighbour as a risky source of terrorists.

Mr. Abassi is the third suspect linked to the alleged train-attack scheme that was made public last month. He was arrested by U.S. authorities in late April, but this only came to light Thursday when a federal indictment against him was unsealed.

Mr. Kenney, speaking at a policy announcement in Mississauga, Ont., confirmed in response to a media question that Mr. Abassi – a one-time student in Canada – had returned to Tunisia and was subsequently denied a visa to return to Canada.

"When we became aware of security concerns, he was back in Tunisia and his visa, I think, his study permit, was not renewed. But beyond that I can't really comment," Mr. Kenney said.

Sources told The Globe and Mail that Mr. Abassi left Canada for Tunisia at the end of 2012. They said the Tunisian national applied to return to Canada in the months that followed, but that Ottawa rejected his visa application because Canadian security agencies had concerns about him.

Mr. Abassi travelled to the United States in mid-March.

A U.S. Customs & Border Protection spokesperson referred questions about why Mr. Abassi was allowed to enter the country to the U.S. Attorney's Office. The U.S. Attorney's Office for the Southern District of New York, which is handling the prosecution, declined to comment on that particular matter.

Prosecutors in New York have said Mr. Abassi is charged with attempting to get false work documents so he could live in the United States and kill Americans.

"Ahmed Abassi had an evil purpose for seeking to remain in the United States – to commit acts of terror and develop a network of terrorists here," U.S. attorney Preet Bharara said in a statement Thursday.

The charges say he was spotted in New York with Chiheb Esseghaier, a fellow Tunisian science student also residing in Quebec.

On April 22, they were arrested on opposite sides of the border. The RCMP nabbed Mr. Esseghaier, 30, in Montreal and accused him of taking part in an "al-Qaeda-supported" plot to derail a passenger train crossing the Canada-U.S. border. He and Raed Jaser, 35, of Toronto, also face terrorism-related charges in the alleged Via Rail scheme that the RCMP have called a plot guided by al-Qaeda elements in Iran. Their arrests were announced immediately by Canadian authorities.

The FBI took Mr. Abassi into custody very quietly in New York, grilling him for a week without any scrutiny from media or defence lawyers.

Bousselham Echchahed, a research assistant at Laval University's faculty of science and engineering, told The Globe and Mail that for several weeks Mr. Abassi had been in contact with his research director, professor Trong-On Do, who was eager for the student to get a Canadian visa and complete his degree.

Mr. Abassi was scheduled to make a presentation on nanoparticles and oxidation at the annual conference of Association canadienne-française pour l'avancement des sciences, or ACFAS, at Laval University this week.

"He never made it to the ACFAS conference, so I had to give the presentation for him," Mr. Echchahed said.

Reached at his home in Quebec City, Mr. Do refused to answer any questions.

University officials and professors declined to make any comments.

"I didn't know Ahmed on a personal level. I answered his questions about the research project and helped him whenever I could. Every Friday he would go and pray and that is all I know about him," Mr. Echchahed said.

Sabrina Shroff, a New York lawyer acting for Mr. Abassi, says the U.S. charges are highly questionable. She suggested that Mr. Abassi, who arrived in Canada from Tunisia on a student's visa in 2010, could never have set foot in the United States without security officials' permission or advance knowledge.

"It certainly raises a question about the government," she said. "… Aren't they the ones that issued him a visa?"

U.S. prosecutors say that Mr. Abassi was under surveillance from the time he entered the United States in mid-March until the time of his arrest on April 22. Along the way he was taped making remarks by an undercover FBI officer he had considered a confidant.

Prosecutors further allege that Mr. Abassi made other incriminating admissions during a week-long period in custody after his arrest, where he faced FBI questioning without a lawyer present.

"We would not agree that he waived his Miranda rights," Ms. Shroff said.

The Canadian government is very sensitive to accusations that terrorists or accused terrorists enter the U.S. through Canada.

Canadian politicians and diplomats spent years after the Sept. 11, 2001 terror attacks correcting the erroneous impression in the United States that the 9/11 plotters entered the U.S. through Canada.

With a report from Kathryn Blaze Carlson in Toronto