Among the assistance that will be untouched, officials said, are programs to train and educate Egyptian military officials in the United States; the delivery of spare parts for many American-supplied weapons; and aid for health care, education and the promotion of business in Egypt.
The administration conveyed the news in a phone call on Wednesday from Defense Secretary Chuck Hagel to Gen. Abdul-Fattah el-Sisi, the army chief who led the ouster of Mr. Morsi. American officials portrayed the phone call as friendly.
The administration also continued to take the position that it was not obligated to classify Mr. Morsi’s ouster as a coup — a judgment that could have required a wholesale suspension in aid. The aid that the administration is holding back, officials said, could be restored if Egypt’s interim leaders take steps toward restoring democracy.
The announcement laid bare the underlying calculations that have shaped the United States’ effort to respond to the upheaval in Egypt ever since the crackdown began in July, leaving more than 1,000 people dead.
American officials have long doubted that cutting back military aid would have any effect on the behavior of Egypt’s military-backed government. The United States also does not want to jeopardize security interests in Egypt, notably counterterrorism efforts, the stability of the Sinai Peninsula and the 1979 peace treaty between Egypt and Israel.