Mr Trump sent out a series of tweets criticising San Juan mayor Carmen Yulin Cruz for criticising his administration's hurricane response.
The mayor has accused his administration of "killing us with the inefficiency", and implored Mr Trump to "make sure somebody is in charge that is up to the task of saving lives".
The US leader has pledged to spare no effort to help Puerto Rico recover from Maria's ruinous aftermath, and is set to visit the island early next week.
He responded to the mayor's criticisms by citing her "poor leadership ability", and also took aim at other officials in the US territory who he said had not been able to "get their workers to help".