In tweets, he accused Puerto Rico of a "total lack of accountability", adding that "electric and all infrastructure was disaster before hurricanes".
The island, whose 3.4 million residents are US citizens, is 90% without power, some three weeks after Hurricane Maria.
On Thursday, Congress approved a $36.5bn (£28bn) disaster relief bill.
The cross-party bill, which still requires Senate approval, provides emergency storm relief for Puerto Rico, Florida, Texas and the US Virgin Islands, as well as wildfire-ravaged California.
What is Trump's plan for Puerto Rico?
In Thursday's morning tweets, the US president noted it was up to "Congress to decide how much to spend".
But he added: "We cannot keep FEMA, the Military & the First Responders, who have been amazing (under the most difficult circumstances) in P.R. forever!"
The mayor of Puerto Rican capital San Juan said Mr Trump's tweets highlight his "desperation" and the "inadequacy" of the hurricane response.
"It is not that you do not get it," Carmen Yulin Cruz added, "it is that you are incapable of empathy and frankly simply cannot get the job done."
White House chief of staff John Kelly said later the US would stand with Puerto Rico "until the job is done".
He also said the president was "exactly accurate" to assert that federal personnel are "not going to be there forever".
Photo copyright: AFP (Caption: A householder in the storm-hit ruins of her home in Aibonito, Puerto Rico)