Mr. Booher insisted on Wednesday that FEMA was not backtracking on its food and water aid plans in response to public criticism. Had the agency planned to end the assistance, it would have required giving notice to the Puerto Rican government, Mr. Booher noted, and FEMA had no plans to end the aid without consulting with Puerto Rico. A statement on Tuesday from Héctor M. Pesquera, the island’s public safety secretary, said that the government had not been informed about any cutoff before the NPR report.

Ending the emergency aid would require a transition of at least two weeks between the federal and Puerto Rican governments, Mr. Pesquera added. FEMA has been distributing water bottles, snack food boxes and ready-to-eat meals to Puerto Rican municipalities, where local mayors have handed them out to needy residents.

On Wednesday, Gov. Ricardo A. Rosselló told reporters in San Juan that his administration had reached out to the homeland security secretary, Kirstjen Nielsen, whose department oversees FEMA, to ensure the aid would continue. FEMA’s plans, Mr. Rosselló said, had been “perhaps miscommunicated.”

Puerto Rico intends to rely on mayors to let his administration know when their residents no longer need emergency food and water, Mr. Rosselló said.

“You can’t pretend to end it overnight,” he said.

The local FEMA workers cited by NPR on Monday — Alejandro De La Campa, the director of the agency’s San Juan-based Caribbean division, and Delyris Aquino-Santiago, a spokesman — mistakenly thought that the date being used in a planning exercise for what ending aid would look like was real, Mr. Booher said.

The reported cutoff date had baffled Washington lawmakers. While major cities like San Juan have had much of their power restored — allowing people to refrigerate their food — some towns in the island’s mountainous interior are still in the dark.

“Cutting this aid to the people of Puerto Rico, almost a third of them who still do not have electricity — it’s unconscionable, and it’s a travesty,” Senator Bill Nelson, a Florida Democrat, said on the Senate floor on Tuesday. Thirty lawmakers from both parties had signed a letter imploring FEMA to change course.

In clarifying FEMA’s position, Mr. Booher noted that the agency’s aid has become less necessary as supermarkets and restaurants return to regular business. The agency has full stockpiles of food and water to distribute to towns and does not need to bring new supplies to the island for now, he said. FEMA has provided more than $1.6 billion in food and more than $361 million in water, in addition to more than 100,000 liters of water, he said.