A recent dispute over why the Metropolitan Museum of Art bookstore decided not to carry a book that closely relates to one of the museum’s current exhibitions has raised questions about the management of the bookstore and the role of the retail division within the institution.

A former bookstore employee has said that a buyer’s decision — since reversed by higher management — not to carry Nicholas Fox Weber’s “The Clarks of Cooperstown,” because it discusses Alfred Corning Clark’s homosexuality, was at odds with the bookstore’s central mission, which is to make money, and was part of a general atmosphere of homophobia in the store. The employee, James Grissom, also said the museum’s leadership has fiercely resisted efforts by the retail employees to unionize.

About the question of unionization, the Met’s spokesman, Harold Holzer said, “We don’t comment on things of that nature.” As for the accusation of homophobia, he said, “Nobody has ever heard of this. Nobody recognizes that it’s an issue at this museum.”

Mr. Grissom quit last Friday, the same day that an article in the New York Times reported that the bookstore was not carrying Mr. Weber’s book, despite a deal made with the publisher, Alfred A. Knopf, that the bookstore would carry it in conjunction with the Met’s exhibition “Impressionist and Early Modern Paintings: The Clark Brothers Collect.” The book is now on sale, and, according to Mr. Holzer, was the day before the article appeared.

Mr. Holzer told the Times that Mr. Weber’s book was held back as a marketing strategy to promote the museum’s own catalog. But a series of e-mails among the bookstore staff, acquired by The New York Sun, show that, at the bookstore level at least, a decision had been made not to carry the book at all.

In an e-mail dated May 15, an assistant book buyer wrote to the bookstore managers:

“Just an FYI in case anybody asks, as it may seem odd that we do not have it … Random House just released a new book called the ‘Clarks of Cooperstown.’ We are not going to carry it … People may ask (and the author may wander in asking about it). Maybe the staff can get a quick briefing from you so they have a heads-up too?”

A manager replied, cc’ing booksellers: “If anyone asks about the new book ‘Clarks of Cooperstown,’ just feign ignorance. We need to sell our catalogue.”

Yesterday, asked by the Sun, Mr. Holzer said a decision was made to carry Mr. Weber’s book “as soon as it was brought to the attention of others within the museum.”

The Met’s retail division, which includes a national network of stores, is somewhat anomalous: a profit-guided institution within a not-for-profit museum. In a recent book of interviews by Danny Danziger with Met employees, “Museum,” the vice president and general manager of merchandise and retail, Sally Pearson, who before coming to the Met worked at Saks Fifth Avenue and Liz Claiborne, says: “My mission is to make as much money as possible, in the most creative and tasteful way possible, to help fund the education programs and to pay the operational costs of the museum.” All of the revenue — almost $40 million in gross profits in fiscal year 2003 (the latest tax records that were publicly available on Guidestar) — goes back into the museum’s operations.

Mr. Grissom said there was an attempt two years ago to unionize the retail employees, but the museum’s leadership “went into a stealth campaign,” promising they would make the changes the workers were requesting. “But they didn’t. They didn’t give raises, they cut people’s hours. I would get calls at 9 in the morning on a day when I was supposed to be there at 11 saying ‘Don’t come in.'” Now, he said, the employees are organizing again, which is “terrifying” to the museum’s leadership.

Retail employees at some other city museums are unionized. Those at the Museum of Modern Art, for instance, are represented, along with other non-management staff, by Local 2110, which is affiliated with the United Auto Workers.

Mr. Grissom said he left both because of the irregularity of his hours and the unpleasant atmosphere created by the bookstore managers. He asserted that another book, Michael Gross’s “740 Park,” about the residents of one of the Upper East Side’s fanciest co-ops, was also removed from the shelves for reasons of homophobia. Mr. Grissom said that when he asked a manager why “740 Park,” which had been selling well, was pulled, he was told that the book was “‘a horrible embarrassment'” to one of the Met’s curators, Everett Fahy, because it described his relationship with a man.

Mr. Holzer characterized Mr. Grissom’s story about “740 Park” as “totally off-the-wall.” “Nobody’s required to keep a book on offer forever,” he said. “We carried it for quite a while.”

In some cases, the museum’s leadership apparently does play a role in deciding whether or not to sell a book. Mr. Grissom said that, at the time of the “Diane Arbus Revelations” show in 2005, the museum acceded to a request by Ms. Arbus’s daughter, Doon Arbus, that it not sell Patricia Bosworth’s unauthorized biography of Arbus during the exhibition. Mr. Holzer declined comment on this matter.

The Met also apparently attempts to exert control over books published about the museum. An item in New York Magazine noted that Mr. Danziger’s book, which Mr. Holzer said will be sold at the museum, was scrubbed of some of its spicier bits after the first galleys were printed.

And the decision to remove “740 Park” from the bookstore may have had less to do with homophobia than with the fact that Mr. Gross is now working on his own book about the Met. Early last year, he met with the Met’s director, Philippe de Montebello, and its president, Emily Rafferty, to ask for their help. But the same week his book was apparently removed from the bookstore, Mr. Gross said, he received a letter saying they had decided not to cooperate with him, and that they were instructing museum employees not to speak to him, either.