It did not provide a specific explanation for their dismissal, but Abadi has been sacking and retiring a raft of top security officials since he took office three months ago.
"New officers were appointed as part of the drive to reform the security apparatus... and improve its efficiency in confronting terrorism," the statement said.
Signup to our newsletter and follow us on Facebook and Twitter!
The latest announcement came a day after he announced that a graft probe had uncovered the existence of 50,000 "ghost soldiers" on the army's payroll.
His spokesman said that the drive to curb corruption which observers said reached unprecedented heights under his predecessor Nuri al-Maliki would spread to all state institutions.
Abadi has already fired or retired several generals who were seen as responsible for the armed forces' abysmal performance when the Islamic State group swept through swathes of Iraq in June.
He also dismantled the office of the commander in chief, an extra-constitutional body which Maliki had set up to retain effective control over the interior and defence ministries.