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WASHINGTON -- As many as 95 percent of Marines would be uncomfortable serving alongside openly gay troops, the retiring commandant of the Marine Corps told Fox News in an exclusive interview.

Gen. James Conway told Fox News' Jennifer Griffin that a majority of his men and women think a repeal of the "Don't Ask, Don't Tell" policy barring gays from serving openly will be problematic, so he has to believe that, too.

"When we take a survey of our Marines, by and large, they say that they are concerned that it will cause potential problems with regard to their order and discipline -- that it will impact their sense of unit cohesion," Conway said.

Gen. Conway was the first member of the Joint Chiefs of Staff to speak out against a repeal earlier this year after Defense Secretary Robert Gates and Joint Chiefs Chairman Admiral Mike Mullen publicly endorsed President Obama's desire to change the law.

Conway plans to retire Oct. 22 after 40 years of service with the Marines. He's only the second Marines chief ever to serve his entire tenure as commandant during wartime.

And wartime, he said, is "probably not the time" to change the military's policy on gays.

Right now, there are 20,000 Marines serving in Afghanistan. Conway told Fox he "wouldn't hazard a guess" as to how many are gay, but he think it's a small percentage, in the "low single digits."

Conway says these few gays don't cause a problem now because their homosexuality is not known publicly. But he said if their sexuality does become public, "90 to 95 percent of the Marines" he has informally surveyed are concerned about the consequences. Conway cited impromptu surveys he has conducted by a "show of hands" among Marines at town hall style meetings.

Late Thursday, Obama's Justice Department requested that California U.S. District Judge Virginia Phillips allow the military to continue enforcing the gay ban during the appeal of her landmark ruling Tuesday, which declared the law unconstitutional.

The move amounted to an admission from the White House that they would not let this policy be legislated in the courts, that it had to be decided by Congress. Congress has failed once already this year to pass a change the law, even with a majority of Democrats in both houses and with public opinion polls that slant heavily toward a repeal.

Gen. Conway agrees that only the Congress should have that ability. "I think that the Congress represents the will of the people," he said. "And we are a nation of laws. The military abides by the laws. And I think we would be much more comfortable, if it's going to change, it comes as a result of the change to the law, not an independent judicial determination in a district somewhere in California."

Meanwhile the military finds itself in the awkward position of having to abide by an injunction that calls on the government "immediately to suspend or discontinue any investigation or discharge, separation or other proceeding that may have been commenced under "Don't Ask, Don't Tell."

Conway says this unfortunately creates "an element of uncertainty" among commanders in the field about how they should handle existing cases.

IRAQ AND AFGHANISTAN

Conway is known for being outspoken, sometimes a renegade, and didn't always agree with the advice being given from the field about the way ahead in Iraq and Afghanistan. He often butted heads with Gen. David Petraeus over the surge in Iraq.

"Frankly, David Petraeus and I disagreed a little bit on this," Conway said. It was Conway's belief that the Marines stationed in Anbar were well on their way to turning the war's momentum. "So we have said that the surge reinforced successes that were already happening in the Anbar."

Conway also weighed in on the controversial July 2011 date that President Obama has set for the start of a troop withdrawal in Afghanistan, saying his Marines serving in the more violent southern regions of Helmand and Kandahar won't be affected by it. "There is an expectation in some regards that it is a precipitous event -- and in fact I think it will be hardly noticeable, probably especially in the south," Conway said. "If you accept that conditions will drive our drawdown it's not logical then that we would start drawing down at first."

Commanders in Afghanistan have argued strongly in recent days that reconciliation with senior Taliban leaders could be the way to end the war in Afghanistan. Some have even compared it to the Anbar Awakening, when Sunni sheiks turned against Al Qaeda and joined forces with the U.S. But Gen. Conway didn't seem sure now is the right time for talks.

"In Iraq, you had what we call a single bellybutton -- a leading sheik, if you will, that influenced thousands or maybe even tens of thousands of people," Conway said. "The Afghan tribal fabric is much more disparate than that. And so one tribal sheik does not necessarily control the thoughts and emotions of -- of thousands."

Conway told Fox News, however, that reconciliation with lower level fighters is feasible and will eventually be necessary. But to engage in those talks now he said, "may be a bit early."

As for the extremist threat coming from the tribal areas of Pakistan, Conway said it's a reason for concern. "Pakistan is a nuclear-armed country and if you are concerned about the nexus of nuclear weapons and terrorism, as we all should be, Pakistan represents the closest danger in that context."

RETIREMENT

When he leaves on Oct. 22, Gen. Conway says he has plans to retire to a log cabin he and his wife, Annette, built in Pennsylvania. His office in the Pentagon is decorated with a Norman Rockwell painting, antique muskets, a five-pound small-mouth bass he caught in Fredericksburg, Va. Before leaving, he reflected on lasting memories he'll take from his service.

One of his biggest successes while serving the Marines, he said, was getting his men and women vehicles that protected against the insurgent's deadliest weapon: roadside bombs. Mine Resistant Ambush Protected vehicles, or MRAPS as they are known, have become a staple for U.S. troops in Iraq and Afghanistan. Their heavy V-shaped hull has saved thousands of lives according to Conway. The program was so successful that in 2007 Defense Secretary Robert Gates expanded the program beyond the Marines to include the Army.

Annette Conway has been a tireless advocate for wounded Marines and their families. The only real regret Gen. Conway says he has is that Marines have been killed or wounded. Gen. Conway told Fox News about a recent visit he and his wife made to meet with wounded Marines.

"We were just at the hospital again yesterday. And each one is -- is just special. Each one has his own or her own story, as the case may be," he said. "And you just hate to see a young man at that point in his life, this is a life-changing event that he's going to have to live with for the rest of his time. That said, their attitude is just incredible. You go out there thinking your going to pump them up and just the opposite takes place because they're such warriors that they're -- that it's just incredible."