"We have continued to urge the interim government officials and security forces to respect the right of peaceful assembly. That obviously includes sit-ins," State Department spokeswoman Marie Harf told reporters.
"We've made that point publicly and privately, and we'll continue to do so," she said.
She declined to state whether the United States specifically raised concerns about the latest orders.
The United States has repeatedly called on Egyptian authorities to exercise restraint after the army on July 3 threw out Morsi, an Islamist who was the country's first democratically elected leader.
But President Barack Obama's administration has refrained from calling Morsi's overthrow a coup, a designation that would require the United States to halt its $1.5 billion in annual aid to Egypt.
The Senate easily rejected a bid to end assistance by Senator Rand Paul, a staunch critic of US foreign aid and star in the conservative populist Tea Party movement.
The Kentucky lawmaker took to the Senate floor to denounce Obama for not identifying Morsi's ouster as a coup and allegedly ignoring urban blight at home in cities such as Detroit.
"When a military coup overturns a democratically elected government, all military aid must end. That's the law. There is no presidential waiver," Paul said.
"So when the military coup occurred in Egypt, how did the President respond? How did Congress respond? The President and his cohorts in Congress responded by shoveling good money after bad into the failed state of Egypt.
"The President is intent on building nations abroad and not taking care of our nation here at home," he said.
But the amendment went down 86-13, with more than half of Paul's fellow Republicans supporting assistance to Egypt.
Senator Bob Corker, the top Republican on the Senate Foreign Relations Committee, said cutting off the aid now would only fuel further instability.
"We should be the steady hand that pushes Egypt toward a peaceful transition to democracy without undermining our interests or Israel's security, especially when conditions in the region are as they are today," Corker said in a statement.
The State Department also backed aid, with Harf saying that it was "important to our national security interests and to our goal of advancing Egypt back towards an inclusive democratic process."
US ally Israel has been supportive of maintaining assistance, believing that the army can help maintain peace and curb militants.
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