The foreign ministry said it "regrets the decision" to reduce some funds allocated under a US assistance programme and withhold the disbursement of other military aid.
It provided no details of the cuts, but US media reports said Washington on Tuesday denied Egypt $96 million in aid and delayed $195 million in military funding because of concerns over its human rights record.
"Egypt considers this step as a misjudgment of the nature of the strategic relations that binds the two countries over decades," the foreign ministry said in a statement.
The New York Times quoted the State Department as saying the move followed a lack progress on human rights and a new law restricting activities of nongovernmental organisations.
More From This Section
US President Donald Trump's arrival in office earlier this year initially saw an improvement in relations with Egypt, after his predecessor Barack Obama had given President Abdel Fattah al-Sisi the cold shoulder over rights issues.
Obama temporarily suspended military aid to Egypt after the July 2013 overthrow of Islamist president Mohamed Morsi and a bloody crackdown on Morsi's supporters that followed.
Trump set aside criticism of Sisi's rights record while pledging to maintain support for the key US ally, which receives an annual $1.3 billion in military aid.
Egyptian authorities have been fighting an insurgency based in the north of the Sinai Peninsula, where an Islamic State group affiliate has killed hundreds of soldiers and policemen.
The Pentagon is also concerned with preventing jihadists from crossing Libya's porous border with Egypt.