While bilateral discussions on the naval drills are still being discussed, the exercises would focus on improving Egypt's ability to deal with small boat attacks and general patrol operations of its coastal waters, Chief of Naval Operations Adm. Jonathan Greenert told reporters Thursday.
The Navy has always maintained a strong relationship with Morsi's predecessor, former Egyptian president Hosni Mubarak, but those ties had "atrophied" in recent years as Mubarak's government clung to power, according to Greenert.
The renewed port calls and military drills will help reinforce those ties in a region that has been roiled by a wave of power shifts and revolutions during the Arab Spring movement.
Last February, Mubarak was one of the many Arab leaders ousted from power by that wave.
Plans for U.S. naval reengagement began shortly after Morsi, in one of his first official acts as Egyptian president, reshuffled the country's military leadership last month.
At that time, Greenert said he reached out to Egypt's newly installed naval chief to congratulate him on his new position. In response, the Egypt's top naval officer suggested that it was time to start looking at joint training exercises with the United States.
The deal also comes at a critical time for the Morsi administration, who is leading Egypt's difficult transition to democratic rule in the face of growing anti-American sentiment fueled by rising Islamic radicalism in the country.
On Sept. 11, a mob of protestors stormed the U.S. Embassy in Cairo, breaching the building's outer walls and burning the American flag before being repelled by U.S. and local security forces.
The protest coincided with a suspected terrorist attack against the U.S. Consulate in Libya, which resulted in the deaths of four Americans including U.S. Ambassador Christopher Stevens.
During Tuesday's speech, Greenert was asked if the rise in anti-U.S. attitudes in the Mideast, in the aftermath of the Arab Spring movement, has raised any alarms among Navy leaders.
The Navy's Fifth Fleet is headquartered in Bahrain, which emerged as one of the political hot spots during the movement's peak. U.S. warships also frequently dock at a number of countries touched by the Arab Spring during their operations in the Mideast.
"We're not concerned yet, but we are keeping an eye on it," he replied, adding increased engagements like the ones planned for Egypt will help quell those concerns.
Morsi sacked Field Marshal Mohamed Hussein Tantawi, the powerful head of the country's military, and the chiefs of Egypt's armed forces in August.
Tantawi and the country's top military brass had been part of the ruling military council that had run Egypt since Mubarak was removed from power six months earlier.
The move effectively eliminated Morsi's chef political opposition as well as the massive restrictions the military council imposed on Morsi's administration after his election earlier this year.