The Marine Corps and its civilian leadership at the Pentagon are squaring off in an unusually public dispute over whether integrating women into the corps’s all-male combat units will undermine the units’ effectiveness, or whether the male-dominated Marine leadership is cherry-picking justifications to keep women out.

The military is facing a deadline set by the Obama administration to integrate women into all combat jobs by 2016 or ask for specific exemptions. The Marines, with a 93 percent male force dominated by infantry, are widely seen as the branch with the hardest integration task. The Marine Corps has the most units closed to women and still trains male and female recruits separately.

The tension began last week when the Marine Corps released a summary of a nine-month, $36 million study that found that integrated combat units were slower, had more injuries and were less accurate when firing weapons.

The commandant of the Marine Corps, Gen. Joseph F. Dunford Jr., submitted the corps’s recommendation on gender integration to the secretary of the Navy, Ray Mabus, on Thursday. Pentagon officials said the corps was expected to request an exemption for at least some front-line combat units.

Mr. Mabus, the civilian head of the Marine Corps, has steadfastly said in public statements that the Marine Corps study is flawed and that its summary findings were picked from a much larger study in a manner that was biased toward keeping women out of combat roles.

In an interview Thursday, Mr. Mabus said he planned to push ahead with integration despite the study. “My belief is you set gender-neutral standards related to the job Marines have to do, and you adhere to them,” he said. “It doesn’t matter whether the Marines who meet those standards are male or female.”

Further complicating the dispute is the fact that General Dunford, who will take over next week as chairman of the Joint Chiefs of Staff, will be responsible for submitting recommendations to the secretary of defense for all the armed services, including the United States Special Operations Command. Officials in the Army, Navy and Air Force have suggested they are not likely to seek exemptions on integration.

On the surface, the debate within the Marine Corps has centered on the physical abilities of men and women. But critics say the dispute is also driven by a male-dominated culture that encourages Marines to believe that their esprit de corps will be undermined by the presence of women.

“The Marines have a climate of non-inclusivity and justify it by talking about combat effectiveness, but a lot of it is based on emotion and not fact,” said Lt. Col. Kate Germano, who was removed as the commander of female Marine recruits this summer after she pushed for integration and clashed with male superiors. “A lot of them, especially the older generation, believe integrating women will be disastrous in war.”

A recent op-ed by retired Lt. Gen. Gregory Newbold of the Marines laid out the concerns about integration, saying women posed a threat to the “alchemy that produces an effective infantry unit.”

“The characteristics that produce uncommon valor as a common virtue are not physical at all,” Mr. Newbold wrote in the piece, published in the online magazine War on the Rocks, “but are derived from the mysterious chemistry that forms in an infantry unit that revels in the most crude and profane existence so that they may be more effective killers than their foe.”

He asked rhetorically how mixing men and women of “the most libido-laden age cohort in humans, in the basest of environs, will not degrade the nearly spiritual glue that enables the infantry to achieve the illogical and endure the unendurable.”

Mr. Newbold could not be reached for comment.

Mr. Mabus dismissed the idea that women would erode unit cohesion and lower morale.

“That is almost exactly the same argument made against ending racial segregation in the military, and the ban on gays — that it will ruin morale,” he said in the interview. “And it just isn’t true. We’ve seen that.”

A senior Pentagon official briefed on the Marine Corps study, who was not authorized to speak publicly, said a separate, unreleased study on the same group of Marines, by the Naval Health Research Center, showed that while women scored lower in many physical tasks and had higher injury rates, they scored higher in mental resilience and had fewer mental health problems. The study also found that integrated units rated their unit cohesion at the same levels as all-male units and outperformed male units at making complex decisions, the official said.

The disagreement between the Marine Corps and the Pentagon is a rare public display of tension in a culture that generally values silent professionals.

“I’m struck by how much they aired their dirty laundry in public,” said Michael E. O’Hanlon, a senior fellow at the Brookings Institution specializing in defense issues. “The Marine leadership is definitely dubious and reluctant about this. I think they know they will have to integrate, but they have real concerns about what it will mean to the force.”

Mr. Mabus will make his recommendation to Defense Secretary Ashton B. Carter by January. Mr. Carter recently echoed Mr. Mabus’s belief that women should be able to enter all military careers if they can meet standards set for their tasks.

Some Marines familiar with the corps’s integration study are concerned that changes to current operations could threaten lives. Sgt. Maj. Justin D. LeHew, a decorated Iraq war veteran who oversaw the integration tests, said in a post on his personal Facebook page this week that lowering standards to allow women into combat teams would endanger other Marines. The post was soon taken down, but was published by Marine Corps Times.

“In regards to the infantry... there is no trophy for second place. You perform or die,” Sergeant LeHew wrote. “Make no mistake. In this realm, you want your fastest, most fit, most physical and most lethal person you can possibly put on the battlefield to overwhelm the enemy’s ability to counter what you are throwing at them, and in every test case, that person has turned out to be a man. There is nothing gender biased about this; it is what it is.”

The Pentagon will announce final decisions on integrating the remaining closed positions and occupations and on any approved exceptions around Jan. 1, Capt. Jeff Davis, a spokesman, said.

Captain Davis said that since 2013, some 111,000 jobs that women were previously excluded from had opened up to them, with 220,000 still closed. Presumably, the bulk of those will open come January.