The founder of a nonprofit group that has rented affordable apartments to a generation of New York City college students siphoned millions of dollars from the agency through a shell company, using the group’s money to fly back and forth to a second home in Aspen, Colo., and to pay for a luxury penthouse in Brooklyn, an investigation by the state attorney general’s office has found.

George Scott, the founder of Educational Housing Services, along with his wife, Yun Suk Scott, and the group’s board of directors, agreed to a $5.5 million settlement to resolve the inquiry, the attorney general’s office said on Sunday. Investigators found that the group’s board had acted with what the attorney general called “stunning” negligence in allowing a shell company, which Mr. Scott created, to charge Educational Housing millions of dollars for unnecessary services. The board was also faulted for approving Mr. Scott’s salary: $718,032 in 2010 and as much as $1.4 million in 2007, amounts the attorney general called excessive.

Most of the settlement, which included no admission of wrongdoing, will go toward reducing the students’ rents and improving conditions of their rooms, the attorney general’s office said.

“Siphoning millions of dollars at the expense of college students is deplorable,” Attorney General Eric T. Schneiderman said in a statement. “We have no tolerance for officers and directors who treat a nonprofit organization as a vehicle for personal enrichment.”