During Afghan President Hamid Karzai’s visit to Washington this week, U.S. officials hope to repair their frayed relationship.

But there’s another troubled relationship that’s affecting the Afghan war effort: the tension between senior U.S. military and civilian officials in Kabul. Gone are the days of the Iraq surge when the U.S. commander in Baghdad, Gen. David Petraeus, and U.S. Ambassador Ryan Crocker worked out of the same building, conferred constantly, and even jogged together in the morning.

In Kabul, relations between Ambassador Karl Eikenberry and U.S. commander Gen. Stanley McChrystal are cool, according to many observers. They not only work in separate compounds, but they have very different ideas of how to deal with Karzai — and how the war should be waged.

Eikenberry sent cables to the White House in November that opposed a military surge and were dubious about a counterinsurgency strategy — both supported by McChrystal. He argued that Karzai was not a reliable political partner, that Afghan security forces wouldn’t be able to take over by 2013, and that there weren’t enough resources for the civilian part of the war effort.

After the cables were leaked (source still unknown), Eikenberry claimed that his concerns had been met and that he supported the White House plan for a troop increase. But the tensions between him and McChrystal remain.

Obvious differences

Keep in mind that McChrystal is pursuing a counterinsurgency strategy that was ultimately endorsed by the White House. It emphasizes that the war won’t be won by killing, but must also focus on negotiations and development aid. The troop increase is meant to help provide the security for that aid to be delivered.

Such a strategy requires close civilian-military cooperation, yet the divergence between embassy and military command is constantly in evidence.

One example: McChrystal wants to encourage the creation of local Afghan defense forces if village or tribal leaders volunteer their men to fight insurgents, an option that could help supplement nascent Afghan army troops. Eikenberry has pushed back, reportedly from fear that this might lead to the formation of militias. But if the Afghan army is unready (and the police totally unreliable) isn’t some alternative needed?

Another example of civilian-military tensions is provided by a fascinating Washington Post report in late April: U.S. military commanders want to buy generators and diesel fuel to expand electricity in Kandahar, the second-largest Afghan city and a Taliban stronghold. The idea is that this short-term fix will build support for Afghan government officials as U.S. and Afghan troops try to drive Taliban out of the area.

Eikenberry wants to focus on long-term energy development, and refurbish the Kajaki dam, a project that has failed repeatedly because the area is too dangerous. Why is it not possible to do the short-term project now, and, when security improves, revisit the dam?

Approach to Karzai

Perhaps the most surprising divergence between the two men is their approach to Karzai. Eikenberry the diplomat (who is also a retired general and former U.S. commander in Kabul) has a strained relationship with the Afghan leader. McChrystal, the general, diplomatically praises Karzai in public and has encouraged him to take a more active role in efforts to stabilize Kandahar. The general has perhaps the best relationship with Karzai of any U.S. official.

After the unproductive war of words between the White House and Karzai, the administration seems to have adopted the McChrystal approach of public praise, while reserving tough talk for private meetings.

But it’s disconcerting to see the top two U.S. civilian and military officials working on such different wavelengths. If U.S. strategy in Afghanistan is to be effective, they must work as a team.

That kind of teamwork helped turn around the situation in Baghdad. During the Iraq surge, the construction of a new U.S. Embassy in Baghdad was delayed to provide a new design that included space for Petraeus and more than 100 of his staff. Close proximity was seen as essential, for symbolism and for coordination.

Petraeus and Crocker built a partnership at the top, with a Joint Strategic Assessment Team and many joint task forces. The goal was to force staff from the two disparate cultures — civilian and military — to cooperate at every stage.

Partnership important

It’s true that McChrystal wears two hats, as U.S. commander and also commander of NATO’s International Security Assistance Force. Right now, he is based at ISAF headquarters, perhaps a quarter-mile down the road from the U.S. Embassy, but it might as well be 10 miles for all the visitation that happens. If a good partnership existed, would it be so hard to commute between those two sites?

I haven’t even touched on the complications of having a special emissary for Afghanistan and Pakistan, Ambassador Richard Holbrooke, which muddies Eikenberry’s role and makes Afghans uncertain about who speaks for President Obama.

But more crucial now is to have a U.S. ambassador who can work with the U.S. commander in a partnership that advances our strategy. To operate otherwise only makes the Afghan effort harder. As one shrewd observer of Afghanistan told me, “We’re not going to win the big war if we fight small wars among ourselves.”

— Trudy Rubin is a columnist and editorial board member for the Philadelphia Inquirer. trubin@phillynews.com