The Army Corps’ headquarters did not immediately respond to a request for comment.

“We can only speculate, but I think the tweet gives a clue as to the reason” for the suspension, said Robert Freudenberg, vice president for energy and environment at the Regional Plan Association, an urban research and advocacy group. “This is a president who gets good headlines for his base out of acting against ‘blue’ states, and there’s a disturbing pattern of stalling or trying to end projects that are important to the Northeast.”

Julia Arredondo, a City Hall spokeswoman, called cancellation “unacceptable” and “dangerous.” She urged the decision makers “to reverse course immediately and finish evaluating the options they are considering to protect New York City and the region.”

According to the Corps official in charge of the project, Clifford S. Jones III, it is highly unusual for a Corps project to lose funding after more than three years of work at a cost of several million dollars.

“This doesn’t happen,” Mr. Freudenberg said. “This is an in-progress study.”

In recent months, the Trump administration has tangled with officials in New York — his birthplace and a center of liberal opposition to his policies. It has, for instance, barred New York residents from Trusted Traveler programs, such as Global Entry, because of the state’s immigration policies. The administration may also delay congestion pricing, the state’s plan to charge drivers a fee to enter the heart of Manhattan.

The sea barrier project had drawn criticism because it addressed flooding only from storm surges, not from sea rise and storm water runoff. Some environmentalists and planning experts had criticized the wall options that the Corps was focusing on, saying the structures would create flooding outside the walls and trap pollutants, harming the recovering ecology of the Hudson River and New York Harbor.