The fallout from the friendly fire incident in Pakistan yesterday that allegedly killed 28 Pakistani soldiers continued today. Not only has the Pakistani government halted supplies going into Afghanistan, they have now denied the use of an air base from which drone attacks were thought to be launched.

This is a potentially significant setback in the war against al-Qaeda and the Taliban in Pakistan. The Shamsi air base has long been rumored to be a major base for drone attacks inside Pakistan.The longer distances we must now use from bases in Afghanistan complicate the strikes making them less likely to succeed.

Fox News:

The government urged the U.S. to leave the Shamsi Air Base within 15 days. The U.S. is suspected of using the facility in the past to launch armed drones and observation aircraft. Pakistan made a similar demand over the summer, though officials reportedly claimed the CIA had already suspended its use of the base as a staging ground for armed drones months earlier.

"Senior U.S. civilian and military officials have been in touch with their Pakistani counterparts from Islamabad, Kabul and Washington to express our condolences, our desire to work together to determine what took place, and our commitment to the U.S.-Pakistan partnership which advances our shared interests, including fighting terrorism in the region," the White House said in a statement Saturday.

Still, the tone of the Pakistani government's statement Saturday underscored the depth of the potential fallout after Pakistan accused NATO aircraft of firing on two army checkpoints and killing 24 soldiers. The incident early Saturday quickly exacerbated tensions between the two countries and threatened to escalate into a standoff more severe than one last year after a similar but less deadly strike.

Last year, Pakistan closed the Torkham border crossing to NATO supplies for 10 days after U.S. helicopters accidentally killed two Pakistanis. On Saturday, Pakistan went further, closing both of the country's border crossings into landlocked Afghanistan.

A short stoppage may have little effect on the war effort, but could have deadly consequences. During last year's dispute, militants took advantage of the impasse to launch attacks against stranded or rerouted trucks carrying NATO supplies.

Contractors are mostly responsible for bringing supplies over the border and they are the ones who will bear the brunt of any Taliban attacks on the stranded convoys. The blocking of supplies by the Pakistani government is one more reason that we must find alternate supply lines through central Asia in order to assure an uninterrupted flow to our forces in Afghanistan. Our people fighting in Afghanistan cannot be held hostage to the political whims of the Pakistanis who are overreacting violently to this incident.

They are accusing the US trying to destroy Pakistani sovereignty. That's nonsense. If we wanted to destroy their sovereignty we wouldn't be bombing two insignificant border posts - posts we had no idea had been set up by the Pakistani government because they were constructed two days ago. If we were after their "sovereignty," there would be no doubt about it.

Word is that the Pakistani troops at the border posts fired on NATO forces in the area who then may have called in air support - not realizing that the forces were Pakistani. To turn a tragic accident into a diplomatic crisis shows that there is more to this than Pakistani anger at their dead troops. They've been looking for a fight since we took down Osama. And now they've got one. Pakistani leaders can show how anti-American they are, which will please the Islamists and other extremists, while the military can demonstrate how they won't be ordered around by NATO or the US.

The threat of withholding aid won't do much good. Pakistan has been sidling up to China during the last year and could probably get comparable military assistance from them if we cut them off. The economic aid will be harder to replace but the Pakistani government may just see that as the cost of scoring points against us and changing the nature of our relationship.

An actual break in relations is not likely. But a further deterioration will mean less cooperation, less trust, and a more complicated peace process in Afghanistan.