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March 2 (Reuters) - Pfizer PFE.N CEO Albert Bourla said the company "has a problem" with the U.S. Food and Drug Administration's biologics and vaccines chief, Vinay Prasad, in response to a question about the drugmaker's recent communications with the regulator.

Bourla said on Monday that Prasad was disregarding the advice of the agency's career scientists.

The regulator's initial refusal last month to review Moderna's MRNA.O mRNA-based flu vaccine and rapid reversal have heightened concerns about internal discord at the FDA and signaled a sharp shift in U.S. vaccine policy under the Trump administration.

In a letter signed by Vinay Prasad, the director of the FDA's Center for Biologics Evaluation and Research, the agency first refused to review rival Moderna's MRNA.O mRNA-based flu vaccine, then reversed course a week later after the company amended its application.

"I think the current director is not following the recommendations of his staff," Bourla said at the TD Cowen healthcare conference.

Internal staff reviewers had supported moving forward with the application initially, according to a Stat report.

Despite Pfizer's issues with the FDA's leadership, Bourla said the company was having "very productive professional collaborations" with the scientists at the vaccine department.