Following months of intense scrutiny of his scientific work, Marc Tessier-Lavigne announced Wednesday that he would resign as president of Stanford University after an independent review of his research found significant flaws in studies he supervised going back decades.

The review, conducted by an outside panel of scientists, refuted the most serious claim involving Dr. Tessier-Lavigne’s work — that an important 2009 Alzheimer’s study was the subject of an investigation that found falsified data and that Dr. Tessier-Lavigne had covered it up.

The panel concluded that the claims “appear to be mistaken” and that there was no evidence of falsified data or that Dr. Tessier-Lavigne had otherwise engaged in fraud.

But the review also stated that the 2009 study, conducted while he was an executive at the biotech company Genentech, had “multiple problems” and “fell below customary standards of scientific rigor and process,” especially for such an influential paper.

As a result of the review, Dr. Tessier-Lavigne said he would retract a 1999 paper that appeared in the journal Cell and two others that appeared in Science in 2001. Two other papers published in Nature, including the 2009 Alzheimer’s study, would also undergo what was described as comprehensive correction.

Stanford is known for its leadership in scientific research, and even though the claims involved work published before Dr. Tessier-Lavigne’s arrival at the university in 2016, the accusations reflected poorly on the university’s integrity.

In a statement describing his reasons for resigning, Dr. Tessier-Lavigne said, “I expect there may be ongoing discussion about the report and its conclusions, at least in the near term, which could lead to debate about my ability to lead the university into the new academic year.”Dr. Tessier-Lavigne, 63, will relinquish the presidency at the end of August but remain at the university as a professor of biology.

The university named Richard Saller, a professor of European studies, as interim president, effective Sept. 1.

The accusations had first surfaced years ago on PubPeer, an online crowdsourcing site for publishing and discussing scientific work. But they resurfaced after the student newspaper, The Stanford Daily, published a series of articles questioning the accuracy and honesty of work produced in laboratories overseen by Dr. Tessier-Lavigne.

As president of Stanford, Dr. Tessier-Lavigne started the university’s first new school in 70 years, the Doerr School of Sustainability. Opened last year, the school’s stated mission is to seek a solution to climate change.

The panel’s 89-page report, based on more than 50 interviews and a review of more than 50,000 documents, concluded that members of Dr. Tessier-Lavigne’s labs engaged in inappropriate manipulation of research data or deficient scientific practices, resulting in significant flaws in five papers that listed Dr. Tessier-Lavigne as the principal author.

In several instances, the panel found, Dr. Tessier-Lavigne took insufficient steps to correct mistakes, and it questioned his decision not to seek a correction in the 2009 paper after follow-up studies revealed that its key finding was incorrect.

The flaws cited by the panel involved a total of 12 papers, in which Dr. Tessier-Lavigne was listed either as principal author or co-author. As a noted neuroscientist, he has published more than 200 papers, focusing primarily on the cause and treatment of degenerative brain diseases. Beginning in the 1990s, he has worked at multiple institutions, including Stanford, Rockefeller University, the University of California, San Francisco, and Genentech, a biotechnology company.

The Stanford Daily first reported claims last November that images were manipulated in published papers listing Dr. Tessier-Lavigne as either lead author or co-author.

In February, the campus newspaper published an article with more serious claims of fraud involving the 2009 paper that Dr. Tessier-Lavigne published while a senior scientist at Genentech.

The Stanford Daily report said an investigation by Genentech found that the 2009 study contained falsified data, and that Dr. Tessier-Lavigne tried to keep its findings hidden.

It also reported that a postdoctoral researcher who worked on the study had been caught by Genentech falsifying data.

Both Dr. Tessier-Lavigne and the former researcher, now a medical doctor practicing in Florida, strongly denied the claims, which relied heavily on unnamed sources.

Noting that, in some cases, it was unable to identify the unnamed sources cited in The Stanford Daily story, the review panel said that The Daily’s claim that “Genentech had conducted a fraud investigation and made a finding of fraud” in the study “appear to be mistaken.” No such investigation had been conducted, the report said.

Following the newspaper’s initial report about manipulated studies in November, Stanford’s board formed a special committee to review the claims, headed by Carol Lam, a Stanford trustee and former federal prosecutor. The special committee then engaged Mark Filip, a former federal judge in Illinois, and his law firm, Kirkland & Ellis, to run the review.

In January, it was announced that Mr. Filip also had enlisted the five-member scientific panel — which included a Nobel laureate and a former Princeton president — to examine the claims from a scientific perspective.

Genentech had touted the 2009 study as a breakthrough, with Dr. Tessier-Lavigne characterizing the findings during a presentation to Genentech investors as a completely new and different way of looking at the Alzheimer’s disease process.

The study focused on what it said was the previously unknown role of a brain protein — Death Receptor 6 — in the development of Alzheimer’s.

As has been the case with many new theories in Alzheimer’s, a central finding of the study was found to be incorrect. Following several years of attempts to duplicate the results, Genentech ultimately abandoned the line of inquiry.

Dr. Tessier-Lavigne left Genentech in 2011 to head Rockefeller University, but, along with the company, published subsequent work acknowledging the failure to confirm key parts of the research.

More recently, Dr. Tessier-Lavigne told the industry publication Stat News that there had been inconsistencies in the results of experiments, which he blamed on impure protein samples.

The failure of Dr. Tessier-Lavigne’s Genentech laboratory to assure the samples’ purity was one of the scientific process problems cited by the panel, which also criticized Dr. Tessier-Lavigne’s decision to not correct the original paper as “suboptimal” but within the bounds of scientific practice.

In his statement, Dr. Tessier-Lavigne said that he had earlier attempted to issue corrections to the Cell and Science papers, but that Cell had declined to publish a correction and Science failed to publish one after agreeing to do so.

The panel’s findings confirmed a report released in April by Genentech, which said its own internal review of The Stanford Daily’s claims did not find any evidence of “fraud, fabrication, or other intentional wrongdoing.”

Most of the panel’s report, about 60 pages, is a detailed appendix of analysis of images in 12 published scientific papers in which Dr. Tessier-Lavigne served either as author or co-author, some dating back 20 years.

The panel found multiple instances of images in the papers that had been duplicated or spliced but concluded that Dr. Tessier-Lavigne had not participated in the manipulation, was not aware of them at the time, and had not been reckless in failing to detect them.

Oliver Whang contributed reporting.