On Saturday, Hagel reached out to the Egyptian military leader, pressing him to end the bloodshed in the country and ensure the tumultuous political transition engulfing Egypt is "as inclusive as possible," Little told reporters at the Pentagon.
Mass protests in Egypt, backed by the country's military over Morsi's hard-line Islamist views, led to the former president's ouster earlier this month.
Adly Mansour was sworn in as Egypt’s interim president on July 4, shortly after Morsi was taken into custody by the Egyptian military.
At the time, al-Sisi also announced the army would be spearheading the creation of a new technocratic government for Egypt.
Little's comments come after a particularly violent weekend in Cairo, in which Egyptian soldiers opened fire into crowds of pro-Morsi protesters pushing for the deposed president's reinstatement as the country's leader.
Recent reports claim nearly 70 Morsi supporters were killed during several mass rallies in Cairo against the new interim government.
Egypt's leaders have a "moral and legal obligation to respect the right of peaceful assembly and freedom of expression," deputy White House press secretary Josh Earnest said Monday.
"The leaders of the interim government of Egypt have promised the Egyptian people and the rest of the world that they are committed to reinstituting a democratically elected government ... through an inclusive process," he told reporters at the White House.
"The violence that we saw [this weekend] certainly is not indicative of that commitment," Earnest added.
That said, Little declined to comment on what specific bargaining tools the Pentagon had at their disposal to pressure al-Sisi to rein in his forces and cobble together a coalition government.
U.S. national security officials and lawmakers on Capitol Hill are continuing to debate whether to proceed with this year's annual $1.3-billion military assistance package to Cairo.
About two-thirds of the military aid to Egypt for this fiscal year has already been obligated, according to Senate appropriators.
The White House has declined to label the ouster of Morsi a coup, which would have required the administration to immediately cut off foreign aid.
To that end, Little did note there were no plans to restart a stalled arms deal between Washington and Egypt.
Last Wednesday, the Pentagon announced plans to indefinitely delay the first deliveries of American F-16 fighter jets to the North African country.
That said, the Pentagon still anticipates completing the F-16 fighter sale to Egypt in the future, a Defense official told The Hill on Wednesday.
"It is our plan to continue delivering these jets in the future," the official said, adding that deliveries of "other defense articles," such as helicopters and other weapon systems to Egypt, will continue unimpeded.
On Monday, Little said Hagel did not discuss plans to lift the ban on the fighter deliveries, but reiterated the Pentagon's commitment to proceed with bilateral military exercises with Egyptian forces, known as "Bright Star," slated for this year.