Donald Trump tweeted that "big decisions" were pending on how to rebuild hurricane-ravaged Puerto Rico as the mayor of the island's biggest city, San Juan, said the response to the disaster was "not a good news story".
Acting Homeland Secretary Elaine Duke had suggested as much a day earlier in the White House driveway, saying the federal response to the aftermath of Hurricane Maria is "a good news story" and adding "the relief effort is under control".
But Carmen Yulin Cruz, the mayor of San Juan, heatedly denied that.
She said on CNN: "This is a people-are-dying story."
Ms Duke was one of several members of the Trump administration on Thursday to hit back against reporting that the federal government was slow to respond to the storm, which knocked out power and left Puerto Rico's 3.4 million people short of food and water.
Mr Trump meanwhile quoted praise from Puerto Rico's governor, Ricardo Rossello, who said the president and the Trump administration have "delivered" for the US territory.
Mr Trump wrote on Twitter: "The fact is that Puerto Rico has been destroyed by two hurricanes.
"Big decisions will have to be made as to the cost of its rebuilding!"
His tweets come after people on the island have said help is scarce and disorganised and food supplies are dwindling in some remote towns.
Mr Trump is expected to survey the damage on the island on Tuesday.