CHAPEL HILL, N.C. — In the summer of 2011, 19 undergraduates at the University of North Carolina signed up for a lecture course called AFAM 280: Blacks in North Carolina. The professor was Julius Nyang'oro, an internationally respected scholar and longtime chairman of the African and Afro-American studies department.

It is doubtful the students learned much about blacks, North Carolina or anything else, though they received grades for papers they supposedly turned in and Mr. Nyang'oro, the instructor, was paid $12,000. University and law-enforcement officials say AFAM 280 never met. One of dozens of courses in the department that officials say were taught incompletely or not at all, AFAM 280 is the focus of a criminal indictment against Mr. Nyang'oro that was issued last month.

Eighteen of the 19 students enrolled in the class were members of the North Carolina football team (the other was a former member), reportedly steered there by academic advisers who saw their roles as helping athletes maintain high enough grades to remain eligible to play.

Handed up by an Orange County, N.C., grand jury, the indictment charged Nyang'oro with "unlawfully, willfully and feloniously" accepting payment "with the intent to cheat and defraud" the university in connection with the AFAM course — a virtually unheard-of legal accusation against a professor. 

The indictment, critics say, covers just a small piece of one of the biggest cases of academic fraud in North Carolina history. That it has taken place at Chapel Hill, known for its rigorous academic standards as well as an athletic program revered across the country, has only made it more shocking.

Two reports on the activities of the African and Afro-American studies department, one internal and one conducted by a former governor of North Carolina, James G. Martin, found problems with dozens of courses and said as many as 560 unauthorized grade changes were suspected of having been made — often with forged faculty signatures — dating back to 1997. The investigations began after a 2012 report by The News & Observer of Raleigh, N.C.

Mr. Nyang'oro, who ran the department for 20 years, remains the mystery at the center of the case. Mr. Nyang'oro, who retired from the university in July 2012, is accused in the reports of teaching dozens of barely existent or questionably led classes and presiding over a department in which grades were illicitly changed, professors' signatures were forged and athletes routinely enrolled in laughably lax classes.

But with each new disclosure, even as his reputation has been savaged, Mr. Nyang'oro has not explained himself.

"Julius has provided no help in answering our questions," said Jay M. Smith, a history professor and a vocal critic of the way the university has handled the matter. "He's been in a cone of silence for the last three years."

Athletes, including many from the popular and revenue-producing football and basketball teams, made up nearly half of the students enrolled in the dubious courses.

The university says the blame rests firmly and exclusively with two people: Mr. Nyang'oro and Deborah Crowder, the department manager, who retired in 2009 after 30 years there.

Ms. Crowder had close ties to the athletic program and has long been in a relationship with a former North Carolina basketball player, Warren Martin. The two reports on the department's activities each named Ms. Crowder as being involved in the infractions. Ms. Crowder, who has not been charged, did not return messages left on her home voice mail.

Some on campus and elsewhere are skeptical that just two people could carry out the questionable activities on their own. "How in the world could a scam like this go on for so long, and no one knew about it?" asked Mr. Smith, the professor.

Michael O. West, a friend and onetime North Carolina colleague of Mr. Nyang'oro, believes the university has made him a scapegoat. "My view is that the university is portraying these two people, Nyang'oro and Crowder, as a couple of rogue employees," Mr. West said.

"But I am sure there were many people in the athletic department and elsewhere who were aware of it," he added. "These two people are being made to take the blame and put out to dry, when the problem was institutional."

Mr. Nyang'oro's lawyer, Bill Thomas, told reporters in December that the case would give his client a chance to explain himself. "There's been one side of this story that has been put forth in the press, but he's going to have an opportunity to present his side," Mr. Thomas said.