A correction to an earlier version of this article is appended to the bottom of the article.

SAN JOSE — An independent auditor will conduct a financial review of San Jose State’s athletic donations in the wake of allegations that school officials misappropriated funds donated for sports scholarship and used them to pay for bonuses for coaches and staff, car allowances and other perks.

San Jose State president Mary A. Papazian announced Friday that she plans to “look closely” into questions about how the university used donations, adding that if the audit shows that the funds were misused, the school will find other money to fulfill the donors’ intent or return the donations.

Earlier this week, the campus newspaper, the Spartan Daily, reported that only 4.4 percent of more than $6.3 million in donations collected over a four-year period by the athletic department’s former fundraising arm, the Spartan Foundation, went toward student scholarships. About 470 student-athletes participate in 22 sports programs under the top level of the National Collegiate Athletic Association, known as Division 1.

In an interview with this news organization Friday, Papazian said the school plans to release the results of the financial review to the public.

The Spartan Daily report has angered San Jose State’s alumni and supporters. But Papazian said, “No student scholarship was denied or withdrawn based on the availability of funds.”

She did not dispute the figures the school paper reported but said they were misleading because all donations earmarked for scholarships went for that purpose.

“We will move forward in as open, transparent and intentional way as possible, to ensure that we honor the requests,” Papazian said.

Allegations of misuse of funds were leveled two years ago in a wrongful termination suit filed in Santa Clara County Superior Court by Elinor Tappe, a former San Jose State assistant vice president of development and executive director of the capital campaigns.

According to the complaint, Tappe “became aware of numerous recurrent instances of misappropriation of donor funding, including funding for the Spartan Foundation Fund, the SJSU Individual Endowments and the Tower Foundation, which were committed, allowed, and encouraged” by school officials.

The suit, settled April 23, alleged that school officials, including Paul Lanning, the chief executive of the Tower Foundation, SJSU’s fundraising arm, misrepresented to donors the real use of money promoted as going toward scholarships.

A day after the suit was settled, the school announced that Lanning had resigned. He could not immediately be reached for comment, but he told the Spartan Daily, “My work to ensure transparency and proper use of donor funds throughout my tenure at SJSU is well documented and verifiable.”

The campus paper’s report said that only about $274,000 was spent on scholarships during the tenure of athletic director Gene Bleymaier and that the scholarship donations were used for other purposes. Bleymaier, in a lengthy email response to this news organization Friday said that the donations were collected to support the entire athletic program, not just scholarships.

“I did not mishandle or misuse any money while at SJSU,” Bleymaier said, adding that the Spartan Daily did not contact him for a response before publishing the article.

Bleymaier said the school never intended for all the money to go to scholarships.

“Donor intent has always been honored,” Bleymaier wrote. “So when the donor’s intent is known, their funds are always spent for their express purpose.”

Bleymaier said he realized when he arrived in 2012 that some staff members who worked to get donations for the university thought that Spartan Foundation funds were used expressly for scholarships.

“I explained that Spartan Foundation funds are used for several legitimate athletic department purposes not limited to scholarships,” said Bleymaier, who in 2017 was moved out of his role as athletic director and reassigned as a special advisor to Papazian.

That message showed up in fundraising appeals as early as 2013, in which the foundation said the money went to scholarships and other athletic department expenses including facilities, travel and salaries. The messaging, however, was inconsistent. In federal tax returns from 2013 through 2015, examined by this news organization, the Spartan Foundation listed its mission as “to raise funds for athletic scholarships for San Jose State student-athletes.” And a description of the Foundation on its website said that scholarship support was its “primary objective.” That description was not changed until earlier this month.

In 2014, the Spartan Foundation was folded into the Tower Foundation, the school’s official gift clearinghouse. Papazian said she was aware of questions about the marketing of fundraising for athletes shortly after taking the president’s job in 2016. She said the school began investigating best practices to ensure that the athletics fund had proper oversight.

But the Spartan Daily reported that contributions for sports continued to go to the athletic department instead of the Tower Foundation. Some of the money was used for car allowances and bonuses for coaches and staff, according to a Spartan Foundation account summary, the school paper reported.

Marie Tuite, SJSU’s current athletic director, did not respond to an interview request.

Papazian said the school spends about $4.5 million annually for athletic scholarships, while the Spartan Foundation in its best years collected $1.5 to $1 million. She said money for athletic scholarships comes from multiple sources.

Donations earmarked for sports are now funneled through the Spartan Athletics Fund, which replaced the Spartan Foundation last year.

Luke Levers, a member of the fund’s executive committee, said he did not know where the money went after it was turned over to the university.

“I support the athletic program, and unless something real drastic were to happen, I would continue to support it,” added Levers, a donor for more than two decades and past president of the Spartan Foundation.

Renowned sociologist Harry Edwards said Friday that the allegations have led to questions from those who have donated to his Institute for the Study of Sports, Society and Social Change, which is housed at San Jose State. He said donors have asked this week for a record of how their gifts to the Tower Foundations were spent.

“It is a troubling situation,” Edwards said in an interview. “There are issues and questions that have to be answered.”

The former SJSU and UC Berkeley professor said he had planned to solicit Silicon Valley companies this year to support the institute.

“This is problematic at this point,” said Edwards, who in 1968 helped organize the historic medal ceremony protest by Spartans sprinters Tommie Smith and John Carlos at the Mexico City Olympics.

The allegations are the latest development calling into question the university’s handling of money for athletics.

In 2016, the school announced plans to resurrect the men’s track and field program and build a $5 million facility on the 50th anniversary of the sprinters’ protest. Last month, university officials said the track is scheduled to close in June to make way for a four-level parking garage, a move that drew the ire of angry alumni and athletes who helped put San Jose State on the sports map.

Tuite and Charlie Faas, the school’s vice president of administration and finance, said at the time that the school failed to raise $2.5 million from private donors to support the track program. The officials said the $2.5 million in student fees earmarked for the program would now be used to build a multipurpose recreational field.