Obama's administration is currently reviewing the status of US assistance to Cairo following the ouster of ex-president Mohamed Morsi and a subsequent crackdown on Islamists.
"You know, my sense is with Egypt is that the aid itself may not reverse what the interim government does," Obama said in an interview with CNN.
"But I think what most Americans would say is that we have to be very careful about being seen as aiding and abetting actions that we think run contrary to our values and our ideals."
The United States gives Egypt USD 1.3 billion a year in military aid along with several hundred million dollars in development and economic assistance.
But he told CNN that after the events in Egypt there was no doubt that Washington could not go back to "business as usual" with Cairo.
He also defended his administration's actions following the coup in July.
He said that the White House did a lot of heavy lifting after Morsi's ouster to try to convince the military to move towards reconciliation but without success.
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