Hagel said he had called General Abdel Fattah al-Sisi, Egypt's defense minister and the central figure in the interim government, to express US concern after yesterday's brutal crackdown on supporters of ousted president Mohamed Morsi.
"The Department of Defense will continue to maintain a military relationship with Egypt, but I made it clear that the violence and inadequate steps towards reconciliation are putting important elements of our longstanding defense cooperation at risk," Hagel said.
"Since the recent crisis began, the United States has made it clear that the Egyptian government must refrain from violence, respect freedom of assembly, and move toward an inclusive political transition," Hagel said.
"Recent developments, including the violence that has resulted in hundreds of deaths across the country, have undermined those principles."
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Due to the US military's decades-long ties with the Egyptian army, Hagel has become the Obama administration's main conduit for communicating with Cairo as the crisis has unfolded.
"In my discussion with Minister Al-Sisi, I reiterated that the United States remains ready to work with all parties to help achieve a peaceful, inclusive way forward," Hagel added.