Allegations of sexual abuse by the longtime president of a leading Chicago-area Islamic school have roiled the region’s Muslims and raised questions about the reporting of sexual abuse in a close-knit religious community.

The allegations that Abdullah Saleem of the Institute of Islamic Education in Elgin, a Chicago suburb, sexually abused an adult female school employee surfaced in December, when a leading Muslim scholar referred to them in a blog.

Elgin police confirmed Saturday that they are conducting a criminal investigation into allegations of sexual abuse at the school, but spokesman Cmdr. Ana Lalley said she could provide no further details.

Saleem, who has been a respected Muslim leader in Chicago for decades, has not been charged with any crime.

Mohammed Kaiseruddin, chairman of the Council of Islamic Organizations of Greater Chicago , the region’s most influential Muslim umbrella group, said Saleem has resigned from his post and been replaced by his son. He said Saleem left for his native India after the allegations surfaced, and he did not know if he had returned.

“I’ve known him for a very long time; it came as a shock to me,” Kaiseruddin said. “Many people found it unbelievable that he would be accused of something like this. I found it unbelievable, too, until I talked to a few other people and got the same story from all of them. Sometimes our weaknesses lead us to do unbelievable things.”

Numerous attempts to reach school officials for comment were unsuccessful.

While the allegations against Saleem are nowhere near the scale of the sexual-abuse scandal faced in recent years by the Roman Catholic Church, they have raised similar painful questions about the relationship between religious communities and law enforcement officials.

Junaid Afeef, a lawyer and Muslim leader in Chicago, said religious and community leaders, especially among the older generation, initially had a “circle-the-wagons” response to the allegations. He said at first they largely ignored them, then chose to investigate them themselves rather than go immediately to the police.

“That’s not their job,” Afeef said. “I wasn’t surprised, but I was a little disappointed.”

“This isn’t the ’80s or the ’90s anymore,” he said. “For a while we insisted on believing that sex abuse and rape don’t happen in our community, because we are Muslims and Muslims don’t do that. But now we know that whatever social ills exists in the broader world, exist in our community, too.”

Some Muslims also worry that public allegations against a prominent leader could compound anti-Muslim sentiment, which Muslim Americans have struggled with since the Sept. 11, 2001, terrorist attacks, and even more so lately with the rise of the Islamic State radical group in Syria and Iraq.

Afeef said that when he started publicly discussing the allegations against Saleem on a popular Listserv, he was criticized by some who told him that he was “playing into the hands of Islamophobes.”

“I’m sure that’s true,” Afeef said. “There are people who have an agenda to malign Muslims. But that’s beside the point. There is a victim here, and her safety and protection trump any bigotry that might result from reporting this.”

The sexual-abuse allegations were raised in December in a blog written by Omer Mozaffar, a leading Muslim scholar who teaches at the University of Chicago and Loyola University Chicago.

Kaiseruddin said the council officials’ initial reaction to the allegations was to investigate the matter themselves. Council investigators went to the school and spoke with at least two other people who corroborated the allegations. He said they also “reported earlier incidents of a similar nature,” without giving details.

“We investigated and talked to several people, and we heard roughly the same story from more than one source,” Kaiseruddin said. “We still have no legal proof, but we know this is not just a rumor started by one person.”

Kaiseruddin said the council then encouraged the alleged victim to file a police report.

“She was reluctant, and her family was reluctant, which is understandable,” he said. “When people report these things, they end up suffering more. We encouraged her. We told her the community is behind you. You should come forward and seek justice. The only way to do that is by reporting it to the police.”

Kaiseruddin said that if the case had involved a minor, the council would have immediately reported it to the police. But because the alleged victim was an adult, he said, they thought it was more appropriate to encourage her to report the crime.

She has since left the school, he said.

“That school was built with community money and the community was benefiting from that school,” he said. “We wanted to see what we could do to help the school come clean and fix any problem they are having. We sat down with them and said they should do a thorough investigation. They hired a law firm and are pursuing an independent investigation.”

Kaiseruddin said the council had also established a task force to help the Islamic schools in the Chicago area create policies to help prevent sexual-abuse cases. He said he is satisfied that the council “did our part.”

“There are many in the community who would like this to stay out of the public arena,” Kaiseruddin said. “But this kind of thing will keep on happening if it is hushed up. We wanted to make sure people are aware of it.”

Amina Saeed, a lawyer and former president of the Muslim Bar Association of Chicago, called the council’s response to the allegations “disheartening and pathetic.”

“They had a golden opportunity to do the right thing on this issue, and they didn’t,” she said.

She said the council should have condemned Saleem’s school for failing to report the alleged abuse to police immediately. Instead, she said, the council was too protective of the school and too reluctant to make the allegations public.

“The Muslim community is like every other religious community in America,” she said. “There is a strong element where people think it is going to bring more shame on us. We don’t need to air this publicly. We can handle it. But it’s just not the case. Religious leaders do not have the training that psychologists, psychiatrists and victims’ advocates have. It’s not their job.”

Saeed said that even though the current allegations come at a time when Muslims are being “vilified,” “that is not a reason to shove this under the rug. It’s not fair to the victim, and the victim is the most important person here. And it’s not fair to our faith tradition.”

Advocates for victims of sexual abuse have also been active in the case.

“The recent allegations of sexual abuse against a religious leader in the Chicago community have elicited much anger and confusion,” wrote Nadiah Mohajir, co-founder and director of HEART Women and Girls, a nonprofit group.

“Our utmost priority is to protect and respect the confidentiality and safety of survivors,” she wrote on her group’s Web site. “That said, we hope that questions from the community will be directed to the rightful source — the staff and Board of the institution in question.”