"We will investigate with depth and sincerity" and hold accountable those who made mistakes or failed to perform their duties, Khaled al-Obaidi said in his first speech since being approved by parliament on Saturday.
"I will not relent in striking corruption and the corrupt, and with God's help, we will work to build a professional military institution."
Obaidi will face major challenges in doing so.
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.
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Prime Minister Haidar al-Abadi has sacked some senior officers, but it will take years to make up the Iraqi military's huge shortcomings in training and discipline.
Corruption is another major problem, with people in some cases buying positions or paying off commanders so they do not have to show up to work.
But the fact that there is a defence minister at all is a positive step -- the post, as well as that of interior minister, were both filled on an interim basis for four years until Abadi's appointment.
But Iraqi forces are so far still struggling to retake and hold territory from the jihadists.