The White House emphasized that the decision did not have implications for $1.5 billion in American aid to Egypt, which it has said it does not want to cut off for now. The administration is reviewing that aid but has scrupulously avoided referring to Mr. Morsi’s ouster as a coup d’état, which could force its suspension on legal grounds.

In the immediate aftermath of Mr. Morsi’s ouster, the administration said it did not plan to halt the F-16 shipment. But officials said they were disturbed by how events have unfolded since then. Holding up planes is a modest, but unmistakable, symbol of that concern — “an inside fastball to the military,” in the words of a Pentagon official.

“We’ve been very clear with the military: we understand this is a difficult situation but we want things to get back on track,” said a White House official, who spoke on the condition of anonymity, citing the diplomatic sensitivities of the decision. “Trying to break the neck of the Brotherhood is not going to be good for Egypt or for the region.”

The warplanes are part of a deal the United States and Egypt reached in 2009 for the delivery of 20 F-16 C/D fighters during 2013. The first batch of aircraft was delivered in January, with more scheduled for this summer and another delivery late this year.

The summer delivery already had been delayed once, for logistical reasons, when it was determined that the American pilots who would ferry the F-16s to Egypt might have difficulty leaving the country on commercial carriers because of the mushrooming political unrest.