Nuri al-Maliki appealed for "self-restraint" but said Baghdad stood with the Egyptian government, describing its moves against the Muslim Brotherhood as efforts to impose law and order.
"We stand strongly with the Egyptian government in its steps to impose the rule of law and install security and peace across all of Egypt," the Iraqi prime minister said in a statement on his website.
Maliki said the ongoing violence in Egypt, which has killed more than 750 people in four days, was the result of a "conspiracy targeting the desires of the Egyptian people".
Arab countries have openly backed the crackdown, with analysts saying most of their leaders tacitly support Egypt's deadly moves as they fear the Brotherhood's growing regional influence since the Arab Spring.
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Egypt's army, directly or indirectly in power since 1952, ousted Morsi as president in a popularly backed July 3 coup and installed an interim civilian government in its place.
Morsi's supporters set up protest camps in Cairo and promised to stay put until the former leader, now in custody, was reinstated.
The death toll from ensuing clashes, in the capital and across Egypt, has topped 750 people.