A spokesman from Mursi's Muslim Brotherhood movement told AFP that two new ministers in the shake-up, which included the finance, oil and justice portfolios, were members of the Islamist movement.
The reshuffle affected both the finance ministry and the international cooperation and planning ministry, which were handling faltering negotiations with the International Monetary Fund for a crucial USD 4.8-billion loan.
Amr Darrag, a senior member of the Muslim Brotherhood's Freedom and Justice Party, was handed the international cooperation ministry, and finance went to Fayyad Abdel Moneim, an Islamic finance expert.
The new ministers were shown on state television taking their oaths before Mursi.
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Opposition leader Amr Mussa denounced the shake-up as "another step towards comprehensive Muslim Brotherhood control".
"A new reshuffle will be required in the near future," he said in an emailed statement. Before the reshuffle, the Muslim Brotherhood had seven of 35 ministers.
A cabinet spokesman told AFP that Mursi had reached out to some parties to supply lists of candidates which were then referred to Qandil.
But opposition parties which had conditioned their participation on Qandil's removal were not consulted, said a senior member of the opposition Wafd party.
The reshuffle is the second major one since Mursi, who won a presidential election in June, named Qandil's government in August.
In January, Mursi replaced 10 ministers, including finance, to "boost the Egyptian economy," after a wave of political unrest forced his government to defer economic reforms demanded by the IMF for the loan.
Egypt's economy, battered by an 18-day uprising that overthrew president Hosni Mubarak in early 2011, has continued to decline amid political unrest despite billions of dollars in aid from donor countries.
The coalition, the National Salvation Front, has conditioned its participation in parliamentary elections in the autumn on Qandil's sacking and a national unity government, demands Mursi has rejected.