His office said that Abadi, who also serves as armed forces commander in chief, and has already sacked a number of senior army officers, dismissed 26 military commanders and sent 10 into retirement.
It did not specify if the officers were in combat units or held administrative posts.
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Abadi also named 18 commanders of new defence ministry posts, his office said, as part of efforts to "reinforce the military along professional lines and fight all forms of corruption".
Defence Minister Khaled al-Obaidi vowed last month to investigate military failings that allowed the Islamic State group to overrun large areas of Iraq and to hold those responsible to account.
IS-led militants launched a major offensive in June, overrunning Iraq's second city Mosul as security forces collapsed en masse, in some cases even abandoning their uniforms and weapons in their haste to flee.
The militants then swept through much of the country's Sunni Arab heartland, where many residents were deeply mistrustful of Iraq's Shiite-led government.