Lt Gen Abdul Wahab Al Saedi, head of the country’s elite Counter Terrorism Service, told a press conference that all those killed wore explosive-laden belts, adding that senior leaders were among the dead.
He named two of the slain field leaders as Barzan Hussein, who served as ISIS's governor of Fallujah, Al Janoob and Rokan Hameed Allawi.
Fourteen others were also identified, he added, but he did not release their names.
The operation took place in the desert to the south of Al Qaim city and involved dropping paratroopers. He added that some militants blew themselves up during the clashes.
In a video released after the press conference, CTS soldiers clad in black uniforms were seen circling a cave in the desert, firing rocket-propelled grenades and tossing hand grenades into it while others attacked with rifles. Some soldiers were later filmed dragging dead bodies and body parts from the cave.
The Deputy Commander of the Joint Operation Command, Lt Gen Qais Al Muhammadawi, said the operation started on February 26 and ended on March 3.
Lt Gen Al Muhammadawi estimated the number of ISIS militants in Iraq was "no more than 400", scattered in rural and remote areas in northern and western Iraq.
A total of 45 militants including leaders have been killed in airstrikes over the past two months, he said.
Remnant ISIS cells have resurfaced in Iraq in recent months, launching a number of deadly attacks against security forces, although the level of violence is low compared with the group’s peak.
Backed by a US-led international coalition, Iraq announced victory against ISIS in late-2017 after three years of gruelling fighting.
Once capable of launching hundreds of attacks across most of Iraq every week, ISIS has carried out attacks in the past year that have been tallied in the dozens, according to Joel Wing, an analyst who has tracked violence levels in Iraq since 2008.
However, the terrorist group's cells continue to mount hit-and-run attacks, particularly in vast desert regions of northern and western Iraq near the border with Syria.
Recent violence has been confined to the western desert, as well as a mountain range in the centre and north of Iraq known as the Jebel Hamrin, and Tarmiya, a restive area north of Baghdad. The group also conducts sporadic operations in Diyala, north-east of Baghdad.
Despite this, ISIS has struggled to launch major attacks in urban areas in recent years and is widely regarded as being in decline in Iraq.