On its website though, GEBN says "there is strong evidence" it is easier to sustain an energy balance "by maintaining an active lifestyle and eating more calories" than "maintaining a sedentary lifestyle and eating fewer calories," since over the long term, attempts to restrict calorie intake are "likely to be ineffective."
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When asked for comment for this article, Coke pointed to a recent post from the company's chief technical officer, Ed Hays.
Regarding the Times article, he wrote, "The story claimed Coke is funding scientific research to convince people that diets don't matter—only exercise. In fact, that is the complete opposite of our approach to business and well-being and nothing could be further from the truth."
In an email, a NYT spokesperson wrote, "We stand by our story 100%."
Addressing the role of Coke at the group, Hill stressed its autonomy.
"The GEBN's research and educational efforts are independent and not subject to pre-approval by the Coca-Cola Company. Industry collaboration with higher education is a common practice today, and the University of Colorado has policies and procedures in place that adhere to high standards of professional and ethical conduct," he wrote.
The controversy comes as Coca-Cola faces declining sales of carbonated soft drinks. Coke's total carbonated soft drink volume dropped 1.1 percent last year while that of Pepsi fell 1.4 percent, according to a report earlier this year from industry publication Beverage Digest.
Coke has acknowledged "obesity concerns may reduce demand for some" of its items, citing it as a risk factor in its latest annual report.
In the same report, Coke wrote obesity "results from poor diets that are too high in calories combined with inactive lifestyles" and is a "complex public health challenge."
Coke rarely discusses the obesity epidemic in calls with Wall Street.
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In the last two years, the company has mentioned the word "obesity" just three times, according to a CNBC analysis of conferences, earnings and guidance call transcripts from FactSet.
This is not unusual among beverage giants. Rival Pepsi didn't mention the epidemic by name once during the period but did discuss a potential sugar tax and a program that emphasizes the importance of balancing calories.
—CNBC's Sara Eisen contributed to this report.