The city schools chancellor, Joel Klein, appears to be rejecting a demand from the president of Columbia University to reverse his decision to remove a Columbia Middle East scholar from a teacher-training program.

In what is shaping up to be a major showdown between two of the city’s top educational leaders, Mr. Klein through a spokesman signaled yesterday that his department is unlikely to yield to the ultimatum from Columbia’s president, Lee Bollinger, that the chancellor rehire scholar Rashid Khalidi as a lecturer in a professional-development program for public-school teachers.

Mr. Bollinger, in a harsh letter to the chancellor, threatened to cut off Columbia’s 10-year-old participation in the program unless Mr. Klein changed his mind. Mr. Bollinger also accused the city’s Department of Education of violating First Amendment principles.

Mr. Khalidi, whose professorship is named for the Columbia scholar and Palestinian activist Edward Said and financed in part by the United Arab Emirates, was among a dozen Columbia scholars lecturing city teachers this semester on how to discuss Middle East politics with their students. Mr. Khalidi, 56, had been participating in the program for two years and spoke to city teachers last month.

“It is my hope that we can resolve this situation,” Mr. Bollinger said in the letter. “If we are unable to do so, I regret that Columbia will have to withdraw from participating in the program in the future. I have asked our General Counsel to contact the Department’s General Counsel to discuss this situation further.”

A Klein spokesman, Jerry Russo, told The New York Sun department officials “will be meeting with Columbia and we will be explaining to them that this is about providing professional development for teachers as opposed to it being an academic freedom issue.”

The education department announced last month that it had terminated Mr. Khalidi’s participation in the program, a day after the Sun reported on the involvement of Mr. Khalidi, who has accused Israel of carrying out “racist” policies, including establishing “an apartheid system” in the West Bank. In addition, while he has repeatedly condemned terrorism against civilians, Mr. Khalidi has said violence against Israeli soldiers serving in the occupied territories constitutes legitimate resistance. Mr. Khalidi was dropped from the program because of “past statements” he made, Mr. Russo said shortly after the department announced its decision February 15.

Mr. Bollinger, in his letter, said the decision was “based solely on his purported political views and was made without any consultation and apparently without any review of the facts.”

“As educators,” the university president said, “I know we both believe strongly that we have a responsibility to uphold the values of tolerance and freedom of expression.”

In defending Mr. Khalidi, Mr. Bollinger is in an effect protecting someone he believes to be a star scholar, who is often said to be carrying on the intellectual tradition of Said, who died in 2003. At the same time, the Columbia president is facing pressure to reshape the Middle Eastern studies department at Morningside Heights.

To a large extent, Mr. Khalidi, who directs Columbia’s Middle East Institute, has remained on the outside of the months-long controversy involving professors in the Department of Middle East and Asian Languages and Cultures who have been accused of intimidating Jewish students. Mr. Khalidi was not mentioned in “Columbia Unbecoming,” the documentary containing interviews with Jewish students that sparked Columbia’s investigation.

In comments to the press, however, Mr. Khalidi has accused the Jewish students of overreacting and has questioned how a Jewish student at Columbia could feel mistreated. The university administration has also tapped him and four other professors to take the reins of the Middle East studies department, giving Mr. Khalidi some power over hiring future hiring decisions.

In a 2001 interview with Los Angeles journalist Jordan Elgrably, Mr. Khalidi was asked about the source of American Jewish support for Israel.

Mr. Khalidi reportedly said: “The mental framework in which they operate won’t allow them to see what’s happening.They can’t accept that this is basically an apartheid system in creation.”

In an interview he gave to CNN in 2001, Mr. Khalidi spoke of Israel’s treatment of Palestinians as “a 35-year-old occupation which has instituted systematic racist policies against 3 million people,” according to a transcript.

Speaking about academic freedom last night at a New York University event, Mr. Khalidi said professors have the responsibility to “use our knowledge to speak to the broader public.” Without mentioning his dismissal from the city program, he said professors are facing a repressive political climate more dangerous than Cold War-era McCarthyism. He declined to speak to the Sun.