Neither the Durham, North Carolina, school nor the local FBI office, which was made aware of the situation at Duke, would specify details of these concerns, but Michael J. Schoenfeld, the university's vice president of public affairs, said the number and tone of the calls were "pretty loud and nasty."
"We have heard from a lot of people who have a lot of interesting and important opinions and perspectives on this," Schoenfeld said.
In a statement Thursday, the school said plans changed because its effort to "unify was not having the intended effect."
The Duke Muslim Students Association had planned to chant the call, or adhan, from the Duke Chapel bell tower. The adhan signals the beginning of the weekly prayer service. Jummah prayers have taken place in the basement of Duke Chapel for many years.
"Duke remains committed to fostering an inclusive, tolerant and welcoming campus for all of its students," Schoenfeld said. "I think when you do these kind of things you like to think and you hope that it will be seen by others as you see them as enlightened ways to introduce diversity and the celebration of faith tradition, but unfortunately it doesn't happen the way you would like it."
Plans for the audible call to prayer have been in the works since fall semester and are not in response to recent criticism of Muslims after the latest terror attacks and arrests, a source with close knowledge of the situation told CNN. The source also said the request did not come from the Muslim community on campus, but rather the university administration.
The university's Imam Abdullah Antepli said his community was disappointed in the school's reversal. But he had praise for Duke, calling its offerings to the Muslim community "far more comprehensive than many other universities in the entire U.S."
Schoenfeld said there will continue to be a call to prayer and service as usual.
"The only thing that has changed," he said, "is that it will not come from the bell tower of the Duke Chapel as previously announced."
There were no shortage of opinions on both sides after the reversal.
Franklin Graham, son of legendary evangelist Billy Graham, applauded the school. Graham had called on donors to withhold support over the plan to allow the adnan, questioning whether evangelical Christians at Duke would be allowed to broadcast their "message across campus."
Others expressed their disappointment in Duke for the reversal.
Omid Safi, head of Islamic studies at Duke University, directed a criticism at Graham.
"Spare me," Safi's Facebook post says, "Spare me the paranoia of a wealthy white male Christian who talks about being marginalized in America."
The Council on American-Islamic Relations, the nation's largest Muslim civil rights group, called the decision unfortunate, saying the university bowed to intimidation.
Members of the Muslim community will now gather on the quadrangle outside the chapel, a site of frequent interfaith programs and activities, before moving to their regular location for prayers. More than 700 of Duke's 15,000 undergraduate and graduate students identify as Muslim.
"Our Muslim community enriches the university in countless ways," Schoenfeld said.
Antepli added, "I see as opportunity, opportunity for people of all faiths, backgrounds and customs to come together and to learn from one another and to love each other."