George Little, a Pentagon spokesman, said the decision was made by President Barack Obama, Stars and Stripes reported.
"Given the current situation in Egypt, we do not believe it is appropriate to move forward at this time with the delivery of F-16s," Little said.
Little did not say whether Hagel set any conditions for the resumption of military aid in his call to Gen. Abdel Fattah al-Sisi.
He suggested the U.S. government is trying to push the current Egyptian government to hold quick elections.
"Moving forward, everything that we do and say will continue to be focused on hastening Egypt's return to a democratically elected government as soon as possible," Little said.
The Egyptian military on July 3 ousted President Mohamed Morsi, who had been Egypt's only democratically elected head of state for about a year. Morsi was replaced by an interim government headed by Adly Mansour, the head of the Supreme Constitutional Court.