WASHINGTON — The Food and Drug Administration is accusing Juul and Altria of reneging on promises they made to the government to keep e-cigarettes away from minors.

Dr. Scott Gottlieb, the agency’s commissioner, is drafting letters to both companies that will criticize them for publicly pledging to remove nicotine flavor pods from store shelves, while secretly negotiating a financial partnership that seems to do the opposite. He plans to summon top executives of the companies to F.D.A. headquarters to explain how they will stick to their agreements given their new arrangement.

Dr. Gottlieb was disconcerted by the commitments the companies made in the deal announced Dec. 19, under which Altria, the nation’s largest maker of traditional cigarettes, agreed to purchase a 35 percent — $13 billion — stake in Juul, the rapidly growing e-cigarette start-up whose products have become hugely popular with teenagers. Public health officials, as well as teachers and parents, fear that e-cigarettes have created a new generation of nicotine addicts.

“Juul and Altria made very specific assertions in their letters and statements to the F.D.A. about the drivers of the youth epidemic,” Dr. Gottlieb said in an interview. “Their recent actions and statements appear to be inconsistent with those commitments.”