There had been many arrests in recent days "targeting specific groups," said State Department spokeswoman Jen Psaki.
These "are not in line with the national reconciliation that the interim government and military say they are pursuing," she told reporters.
"If politicized arrests and detentions continue, it is hard to see how Egypt will move beyond this crisis."
Yesterday, Egypt's public prosecutor ordered the arrest of Muslim Brotherhood supreme guide Mohammed Badie and other top leaders for allegedly inciting violence after 51 people were killed in clashes on Monday.
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The Egyptian public prosecutor has also pressed charges against 200 of the 650 people it detained during the violence, with the others released on bail.
Ousted president Mohamed Morsi has also not been seen in public for more than a week since he was toppled by the military on July 3.
"We have called for an inclusive process moving forward, including all parties. That's where our focus is now," Psaki added.