Morsi – who was thanked by the United States for helping to broker a ceasefire between Israel and Hamas – had been slated to join the Islamabad talks but state TV in Egypt said he would now stay home to monitor the truce.
In Pakistan, officials said they did not know why Morsi was no longer coming, but that Vice President Mahmud Mekki had arrived instead.
"The Egyptian vice president is representing his country at the summit on behalf of President Morsi, who is not coming," said one foreign ministry official on condition of anonymity because he was not authorised to speak to the media.
"I don't know the reason for the change of plans by the Egyptian president at the 11th hour," he added.
Pakistan, which wants to use the D-8 to improve its international standing, had welcomed Morsi's prospective visit as the first by an Egyptian head of state in four decades.
World leaders hope the ceasefire between Israel and Hamas will offer at least temporary respite from bloodshed in Gaza and southern Israel.
Morsi, a leading member of Islamist group the Muslim Brotherhood, was elected in June in Egypt's first election since a popular revolt brought down secular strongman Hosni Mubarak.
He resigned from his Brotherhood-led party, the FJP, and vowed to represent all Egyptians, but his elevation raised concerns about Cairo's peace treaty with Israel and its ties with Hamas, part of the Brotherhood movement.
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