Gee’s extraordinary compensation was discovered as part of a Globe analysis, conducted by Northeastern University investigative reporting students, of data culled from publicly available tax returns filed by more than 22,000 nonprofits in Massachusetts.

Elizabeth K. Keating, a nonprofit finance expert who reviewed the school’s documents, went further: “If I sat down to write a fictional case study that was designed to wave red flags about an organization that is misusing its tax exemption for personal gain, this would be it.’’

The public documents, she said, “raise questions about the appropriate use of charitable funds, as well as the organizational governance process that led to their approval.’’

Attorney General Martha Coakley, who oversees public charities, said Gee’s “compensation, employment contract, and other benefits . . . seem excessive.’’ After reviewing the reports at the Globe’s request, Coakley’s office sent a letter to the school Wednesday demanding information from board members.

Gee, after ignoring the Globe’s calls and e-mails for more than a month, issued a statement Wednesday asserting that his compensation and perks are warranted. He said that they are comparable with those given to leaders of similar institutions, but did not identify any.

For years, the school’s revenues have financed a lavish lifestyle for Gee and for his wife, who has been paid at least $100,000 a year since 2003. And they have vacationed together at school expense: The school owns a deluxe winter getaway in the US Virgin Islands for their use, part of a 17-year employment contract that expires in 2023, when Gee will be 79.

Five months later, the school, which focuses on a particular field of business management, purchased new automobiles to fit the estate setting: a silver Mercedes-Benz S550 sedan for Gee and a silver Mercedes-Benz station wagon for his wife, Aileen Waters Gee. The cost: $130,638, or about 2 percent of the school’s revenues that year.

Gee has champagne tastes. In 2009, he persuaded the Massachusetts Development Finance Agency to authorize $2.64 million in low-interest bonds. That made possible his school’s purchase of a $3.25 million waterfront compound on Oyster Pond with spectacular views of Martha’s Vineyard, especially from the six-bedroom house earmarked to be Gee’s presidential residence.

Yet the National Graduate School of Quality Management awarded its president, Robert J. Gee, $732,891 in compensation two years ago. By comparison, the president of Tufts University, with 10,800 employees and 5,500 students, had nearly identical compensation the same year, $738,596.

FALMOUTH - It is a tiny school, with an enrollment the size of a modest elementary school. There is no campus, just a small office building. Its 400 part-time students are invisible here, attending classes at off-site facilities across the country.

While compensation agreements at nonprofits are supposed to be scrutinized by boards of directors, it is not clear how diligently the National Graduate School’s board carried out its duties. Several board members, including its chairman, Thomas Kneaval of Delaware, refused to discuss their role.

One former member, Scott Adams, said the board was mostly a “puppet group’’ of Gee’s friends. Sometimes, he said, the board was not consulted about important decisions. Often, he said, the board was informed after the fact. It was, he said, “a one-way conversation.’’

Adams, a board member from 2004 to 2007 and subsequently a full-time official at the school, said Kneaval’s attitude seemed to be that it was Gee’s school and the board was to do what Gee wanted. Adams said he does not remember that Gee’s 17-year contract even came to the board for approval in October 2006.

“If that contract came to the board, it would have been rubber-stamped,’’ Adams said.

Gee agreed during a brief telephone interview on April 11 to answer questions, which were sent to him the next day. On April 16, Gee promised to provide answers by Monday of this week, but did not, asking for another delay. Late Wednesday, Gee e-mailed some answers to the Globe, saying they should be attributed to Kneaval, the chairman.

The statement said Gee’s compensation is justified because he is the school’s founder and because he maintains a full teaching load.

The statement said the Oyster Pond compound was never intended to be his residence, even though the school’s own documents, some with Gee’s signature, consistently said it would be. It said his wife’s hiring had nothing to do with her being his spouse. The statement was silent about her Mercedes-Benz.

Gee, who is 67, founded the school in 1994. Its focus is graduate-level coursework in total quality management, the practice of training workers and managers, and even customers and suppliers, to more efficiently manage production and processes. These practices, which helped make Japan an economic superpower, are now widely used by American manufacturers and have become a staple in business school course catalogues.

Keating, who teaches at Boston College and at Boston University and has written extensively about executive compensation, said that Gee’s salary and perquisites are so excessive that the Internal Revenue Service might levy substantial excise tax assessments against the school and Gee. If the IRS finds the violations extreme, she added, the school could be stripped of its tax-exempt status.