Coca-Cola’s top scientist is stepping down after revelations that the beverage giant initiated a strategy of funding scientific research that played down the role of Coke products in the spread of obesity.

Rhona S. Applebaum, Coke’s chief science and health officer, helped orchestrate the establishment of a nonprofit group known as the Global Energy Balance Network. The group’s members were university scientists who encouraged the public to focus on exercise and worry less about how calories from food and beverages contribute to obesity.

Coca-Cola spent $1.5 million last year to support the group, including a $1 million grant to the University of Colorado medical school, where the nonprofit group’s president, James O. Hill, a prominent obesity researcher, is a professor.

Coke’s financial ties to the group were first reported in an article in The New York Times in August, which prompted criticism that the soft drink giant was trying to influence scientific research on sugary drinks.

The university returned the money to Coca-Cola this month after public health experts raised concerns.

Dr. Applebaum, a food scientist with a Ph.D. in microbiology, had been Coke’s chief scientific and regulatory officer since 2004. In that role she helped lead the company’s efforts to work with scientists as a way to counter criticism about sugary drinks.

At one food industry conference in 2012, Dr. Applebaum gave a talk outlining Coca-Cola’s strategy of “cultivating relationships” with top scientists as a way to “balance the debate” about soft drinks.

A spokeswoman for Coca-Cola said on Tuesday that Dr. Applebaum, 61, had made the decision to retire in October and that her retirement “has been accepted and the transition is underway.” The company declined a request for an interview with Dr. Applebaum.

Coca-Cola has said that while it offered financial support for the Global Energy Balance Network, the company had no influence on the group or the scientific research it produced. But reports show that Dr. Applebaum and other executives at Coke helped pick the group’s leaders, create its mission statement and design its website, findings first reported this week by The Associated Press.

The A.P. also published a series of emails between Dr. Hill of the University of Colorado and Coke executives that revealed the initial strategy of the Global Energy Balance Network. Before the G.E.B.N. was created, Dr. Hill proposed publishing research that would help the company fend off criticism about its products by shifting the blame for obesity to physical inactivity.

“Here is my concept,” Dr. Hill wrote to Coca-Cola executives about the study he was proposing, according to the emails. “I think it could provide a strong rationale for why a company selling sugar water should focus on promoting physical activity. This would be a very large and expensive study, but could be a game changer. We need this study to be done.”

In other emails obtained by The A.P., Dr. Hill told executives at Coca-Cola that he wanted to work on the company’s behalf to improve its public reputation. At the time, Coca-Cola and other beverage companies were engaged in a public relations battle, with soda sales declining and cities around the country proposing taxes on sugary drinks, which have been linked to obesity, diabetes and heart disease.

Dr. Hill wrote to executives at the company that it was “not fair” that Coca-Cola was being singled out as “the No. 1 villain in the obesity world.” Dr. Hill added: “I want to help your company avoid the image of being a problem in people’s lives and back to being a company that brings important and fun things to them.”

The emails also show that Muhtar Kent, Coke’s chief executive, wanted to enlist Dr. Hill to help shape media coverage about soft drinks. In an email on Oct. 18, Mr. Kent asked Dr. Applebaum and other top officials at Coke how he might persuade the CBS News host Charlie Rose to invite Dr. Hill on his show. “CBS This Morning” had just broadcast a segment about the amount of exercise required to burn off the calories in a serving of Coca-Cola. Dr. Applebaum replied to Mr. Kent’s email that day with Dr. Hill’s credentials. Dr. Hill did not appear on the show.

On Tuesday, a spokeswoman for Coca-Cola said that Mr. Kent had sent the email because he had been concerned that the news segment “was inaccurate.”

In a statement, Mr. Kent said, “It has become clear to us that there was not a sufficient level of transparency with regard to the company’s involvement with the Global Energy Balance Network. Clearly, we have more work to do to reflect the values of this great company in all that we do.”

Dr. Hill declined a request for comment. But in an interview in August, he insisted that Coca-Cola did not speak for him or his organization. “They’re not running the show,” he said. “We’re running the show.”

In a statement on Tuesday, the University of Colorado School of Medicine suggested it did not see any problems with Dr. Hill’s relationship with Coca-Cola.

“The school of medicine does not prohibit faculty members from communicating with governmental, for-profit or nonprofit entities that provide funding for initiatives intended to improve individual and public health,” the university said. “The school does expect such efforts to be hypothesis-driven and designed to answer questions and not to advance a specific point of view.”

Michael F. Jacobson, the executive director of the Center for Science in the Public Interest, a consumer advocacy group, said it was concerning to see “how a major corporation is using a professor to propagate their views.”

Marion Nestle, a professor of nutrition, food studies and public health at New York University and the author of “Soda Politics,” said that when food and beverage companies pay for research, they do so to aid marketing efforts and to “silence critics.”

Dr. Nestle added, “The Global Energy Balance Network has been a public relations disaster for Coca-Cola.”