On the eve of the opening of Morsi's trial, Kerry was in Cairo to shore up ties with a key ally and ensure it moves ahead on plans to restore democracy, just weeks after Washington partly suspended aid to Egypt.
"We are committed to work with and we will continue our cooperation with the interim government," Kerry told a joint news conference with Egyptian foreign minister Nabil Fahmy, urging "inclusive, free and fair elections".
Kerry also played down Washington's suspension of part of its USD 1.5 billion in annual aid to Cairo, denying the decision had been taken to punish Egypt's military leaders and saying it "is a very small issue between us".
"US-Egyptian relations should not be defined by assistance," Kerry said, adding direct aid would continue to help Egyptians in areas such as health and education and to aid "counter terrorism" efforts.
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In a move that angered Cairo, Washington last month said it was "recalibrating" its aid to Egypt -- including about USD 1.3 billion for military assistance -- and suspending delivery of big-ticket items like Apache helicopters and F-16 aircraft.
During his six-hour visit, he was also hosting an encounter with a broad cross section of civil society groups, including religious groups, human rights advocates, and youth and labour organisations.
The top US diplomat said Washington believed "the US-Egypt partnership will be strongest when Egypt is represented by a democratically elected government".
He condemned violence since Morsi's ouster, but said nothing about Morsi himself.