Dr. José Baselga, the chief medical officer of Memorial Sloan Kettering Cancer Center, resigned on Thursday amid reports that he had failed to disclose millions of dollars in payments from health care companies in dozens of research articles.

The revelations about Baselga’s disclosure lapses, reported by The New York Times and ProPublica last weekend, have rocked Memorial Sloan Kettering, one of the nation’s leading cancer centers, in recent days. Its top executives scrambled to contain the fallout, including urgent meetings of physician leaders and the executive committee of its board of directors.

In his resignation letter released Thursday, Baselga, who also served as the physician-in-chief, said he feared that the matter would be a distraction from his role overseeing clinical care and that he had been “extremely proud” to work at Memorial Sloan Kettering.

“It is my hope that this situation will inspire a doubling down on transparency in our field,” he said, adding that he hoped the medical community would work together to develop a more standardized system for reporting industry ties.

In an email sent to the staff Thursday evening, Dr. Craig B. Thompson, the hospital’s chief executive, said that Baselga had made “numerous” contributions to Memorial Sloan Kettering, patients and cancer treatment. Dr. Lisa DeAngelis, the chairwoman of neurology, will take over as acting physician-in-chief until Baselga’s successor is hired.

The resignation was effective immediately, and he will have no continuing role at the cancer center, although he will stay for two weeks to ease the transition, said Christine Hickey, a spokeswoman for the cancer center.

Thompson echoed comments he made to the hospital staff on Sunday, saying that the cancer center had “robust programs” in place to manage employees’ relationships to outside companies, but that “we will remain diligent.” He added, “There will be continued discussion and review of these matters in the coming weeks.”

Baselga, a prominent figure in the world of cancer research, omitted his financial ties to companies like the Swiss drugmaker Roche and several small biotech start-ups in prestigious medical publications like the New England Journal of Medicine and the Lancet. He also failed to disclose any company affiliations in articles he published in the journal Cancer Discovery, for which he serves as one of two editors in chief.

All told, ProPublica and The Times found that Baselga had failed to report any industry ties in 60 percent of the nearly 180 papers he had published since 2013. That figure increased each year — he did not disclose any relationships in 87 percent of the journal articles that he co-wrote last year.

In an interview and later statement, Baselga said he planned to correct his conflict-of-interest disclosures in 17 journal articles, including in the New England Journal and the Lancet. But he contended that in dozens of other cases, no disclosure was required because the topics of the articles had little financial implication. He also said his failed disclosures were unintentional and should not reflect on the value of the research he conducted.

Baselga and Memorial Sloan Kettering said that he had disclosed his industry relationships to the cancer center.

The New England Journal and the Lancet, as well as professional societies like the American Society of Clinical Oncology and the American Association for Cancer Research, said they were conducting reviews of Baselga’s disclosure practices after inquiries from The Times and ProPublica. Baselga was president of the AACR in 2015 and 2016 and appears to have violated disclosure rules for reporting conflicts of interest during that period.

In his statement Thursday, Baselga said that he took full responsibility for his disclosures and that he had already submitted updates to medical journals “and will continue to do so until the record is complete.”

A spokeswoman for the New England Journal, Jennifer Zeis, said in an email Thursday that Baselga had submitted changes to his disclosures but that editors had questions for him before the articles could be corrected. A spokeswoman for the AACR said that organization was continuing to review Baselga’s disclosures.

Baselga, 59, is an expert in breast cancer research and played a key role in the development of Herceptin, which was developed by Genentech, a subsidiary of Roche. He came to Memorial Sloan Kettering in 2013 after serving as chief of hematology and oncology at Massachusetts General Hospital in Boston. Before that he was a leader at the Vall d’Hebron Institute of Oncology in Barcelona, Spain.

Medical journals and professional societies have imposed stricter rules about reporting relationships to industry after a series of scandals a decade ago in which prominent physicians failed to disclose payments from drug companies. But medical journals have said they don’t routinely fact-check authors’ disclosures, and much is left to the honor system.

Ethicists say that outside relationships with companies can shape the way studies are designed and medications are prescribed to patients, allowing bias to influence medical practice. Reporting those ties allows the public, other scientists and doctors to evaluate the research and weigh potential conflicts.

Jeffrey S. Flier, who was dean of the Harvard Medical School from 2007 to 2016, said medical leaders should be held to a higher standard.

“The higher you are in the organizational structure, the more important it is that you fulfill those obligations,” he said. “You’re not just another faculty, you’re also a faculty to whom other people look up and your reputation is tied to the institution’s reputation.”

That said, he added, relationships between academic faculty members and the health care industry are essential to developing new drugs.

Baselga has extensive ties to a range of companies, including sitting on the board of the large pharmaceutical company Bristol-Myers Squibb and serving as a director of Varian Medical Systems, which sells radiation equipment and for whom Memorial Sloan Kettering is a client.

Baselga has served on the boards of at least four other companies since 2013, and the positions required him to assume a fiduciary responsibility to protect the interests of those companies, even as he oversaw the cancer center’s medical operations. Baselga and Memorial Sloan Kettering have said the cancer center has put firewalls in place to prevent any conflicts.

Baselga received nearly $3.5 million in payments from drug, medical equipment and diagnostic companies from August 2013 through 2017, according to Open Payments, a federal database that tracks payments to physicians from health care companies. Most of that amount, about $3 million, involved a payment from Genentech for Baselga’s ownership interest in a company it acquired, Seragon Pharmaceuticals, in 2014.

But the $3.5 million in the Open Payments database does not include payments from companies that don’t have products approved by the Food and Drug Administration. Such companies are not required to report their payments under federal law.

For instance, Infinity Pharmaceuticals, a start-up with no approved drug, paid Baselga nearly $250,000 in cash and stock options for serving on its board from 2015 to 2017. He declined to disclose how much he received from such companies.

Baselga was one of the highest-paid staff members at Memorial Sloan Kettering, earning more than $1.5 million in 2016, the most recent year for which the nonprofit’s financial filings are available.