Moderna said on Tuesday that the U.S. Food and Drug Administration is refusing to consider its application for a new flu vaccine made with mRNA technology, marking a setback for the company’s plan to bring an updated shot to market through the U.S. regulatory process.

In a company announcement, Moderna said the FDA issued what is called a “refusal-to-file” letter. The letter, the company said, objected to how Moderna conducted a clinical trial that enrolled 40,000 people and compared the new vaccine with a standard flu shot used in the United States.

Moderna said the trial results showed the new vaccine was somewhat more effective in adults 50 and older than the standard flu shot. The company said the FDA nevertheless rejected the application at the threshold stage because, as Moderna described it, the agency does not consider the study to include what FDA requires for an “adequate and well-controlled trial.”

Moderna said FDA vaccine director Dr. Vinay Prasad wrote in the letter that the FDA does not consider the application to contain an “adequate and well-controlled trial” because it did not compare the candidate shot to “the best-available standard of care in the United States at the time of the study.” Moderna said the letter also pointed to advice FDA officials gave Moderna in 2024, during the Biden administration, that Moderna did not follow.

According to Moderna, the 2024 feedback said it was acceptable to use the standard-dose flu shot the company had chosen, but that a different brand specifically recommended for seniors would be preferred for anyone 65 and older in the study. Moderna said it complied with what it was told as to the trial’s setup going forward, while still arguing that the FDA’s later complaint is based on not using the senior-specific recommended brand in the comparison.

Moderna said it also had shared with FDA additional data from a separate trial comparing the new vaccine against a licensed high-dose flu shot used for seniors. The company said the FDA “did not identify any safety or efficacy concerns with our product,” and that the agency “does not further our shared goal of enhancing America’s leadership in developing innovative medicines,” in remarks carried in a statement from CEO Stephane Bancel.

The FDA’s decision to refuse to file a vaccine application is uncommon, the company said, because it usually triggers a longer period of discussions between the manufacturer and the agency. Moderna said it has requested an urgent meeting with FDA.

The company said it has also applied for approval for the vaccine in Europe, Canada and Australia, even as the FDA action blocks the application from moving forward in the United States. The news comes as the AP described the FDA’s posture toward vaccines using mRNA technology as part of broader heightened scrutiny under Kennedy, who has criticized mRNA vaccines before and after becoming health secretary.

In the past year, the AP said, FDA actions under Kennedy included rolling back recommendations around COVID-19 shots, adding extra warnings to the two leading COVID vaccines made with mRNA technology, and removing critics from an FDA advisory panel. The AP also said Kennedy announced plans to cancel more than $500 million in contracts and funding for the development of vaccines using mRNA, and described how FDA has previously relied on shorter flu-vaccine studies that focus on immune responses rather than multi-year outcomes.