The articles themselves, Mr. Cohen wrote, “bear no resemblance to the source materials” they cite. And in the final paragraph of his letter, he refers to the “numerous and productive relationships” that Exxon Mobil has with Columbia. (In 2014, according to Exxon Mobil’s own figures, the company donated nearly $220,000 to Columbia University.) Some read that as a subtle hint that Exxon Mobil might review its relationship with the university. The company said on Tuesday that there was no threat intended.

In his response, Mr. Coll said he had been troubled to discover that Mr. Cohen had “made serious allegations of professional misconduct” even though “you or your media relations colleagues possess email records showing that your allegations are false.” He went on to rebut many of the detailed points in Exxon Mobil’s letter, writing that Ms. Rust gave the company plenty of time to respond to her questions and that the reporters had clearly identified themselves as journalists.

The article was indeed funded, in part, by the Rockefeller Brothers Fund, Mr. Coll wrote, but that fact was disclosed and the fund had no impact on the articles that were ultimately published. Though the accusations are presented as factual errors, he wrote, “in fact what you dispute is the emphasis of the articles. You have dressed up this rather commonplace criticism of investigative reporting in academic clothing.”

“What your letter advocates really is that the factual information accurately reported in the article, and unchallenged by you, be interpreted differently,” Mr. Coll wrote.

Alan T. Jeffers, a spokesman for Exxon Mobil, said on Tuesday that the company felt the articles still fundamentally misrepresented the source documents. When it has tried to engage with The Los Angeles Times it has consistently been referred to Columbia, he said, and the company has asked for an opportunity to meet with university representatives to discuss what possible actions remain available, he said.

The Los Angeles Times said that its editors had “carefully reviewed Exxon Mobil’s complaints and concluded that the articles we published in collaboration with Susanne Rust and her team at Columbia University Graduate School of Journalism were accurate, fair and balanced. We will continue working with the Columbia reporting team to publish journalism on this very important subject.”