The Obama administration publicly backed the revolution that toppled longtime leader Mubarak last year but also sees the Egyptian army as a crucial regional security partner.
The country is also of strategic importance to the United States because of the Suez Canal, a vital conduit for trade and for U.S. military vessels.
Washington released $1.3 billion in military aid for Egypt in March despite misgivings over progress towards democracy, saying U.S. national security required continued military assistance.
Panetta’s visit will underscore the somewhat delicate position the United States faces in Egypt. For three decades it strongly supported Mubarak, who repressed and marginalized Mursi’s allies in the Muslim Brotherhood.
Since Mubarak’s overthrow last year, the Brotherhood has propelled itself to the heart of politics, forcing Washington to put aside its concerns and strengthen its links with the movement.
The Brotherhood has a history of hostile rhetoric towards Israel and its conservative social agenda sits uneasily with U.S. attempts to promote personal freedoms including the rights of women and religious minorities in the Middle East.
Clinton warned on Monday that religious freedom in Egypt appeared to be “quite tenuous”, saying the outgoing interim, army-backed government has failed to aggressively prosecute perpetrators of sectarian violence.