She called for his immediate release from the custody he has been kept in since just hours after the military toppled him on July 3 following nationwide street protests against him.
"I believe he should be released. I was assured he is well. I would have liked to see him," Ashton told reporters.
During her visit, Ashton met the country's new leaders, including interim President Adly Mansour, prime minister Hazem al-Beblawi and the general behind the coup, army chief Abdel Fattah al-Sisi.
She said she also met representatives of Tamarod, the grass-roots movement behind the mass protests that led up to Morsi's overthrow.
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On a visit to Cairo on Monday and yesterday, US Under Secretary of State William Burns did not meet Muslim Brotherhood representatives and was snubbed by Tamarod.
Senior FJP official Amr Darrag said it had been the EU who had sought the meeting.
"The delegation didn't come to ask the EU anything, the meeting took place at Ashton's request," he told the state MENA news agency.
She also stressed "the need to get the economy going as quickly as possible," in a country where a quarter of the population live below the poverty line.
Yesterday, a new 34-member cabinet was sworn in, but both the Muslim Brotherhood and the main Salafist party Al-Nur spurned offers to join it.
As a result, none of the ministers in the caretaker administration are affiliated to the Islamist movements which swept Egypt's first freely contested parliamentary elections.