Even with the reopening of critical supply routes through Pakistan, the U.S. military confronts a mammoth logistical challenge to wind down the war in Afghanistan, where it must withdraw nearly 90,000 troops and enormous depots of military equipment accumulated over the past decade.

The first truck carrying supplies to U.S. and NATO troops entered Afghanistan from Pakistan on Thursday morning, news services reported, two days after Secretary of State Hillary Rodham Clinton’s apology for a deadly U.S. airstrike convinced Pakistan to end a seven-month diplomatic standoff over the border crossing.

Assuming Pakistan doesn’t seal its border again, U.S. and NATO commanders still face the prospect of pulling out at least a third of the cargo from northern Afghanistan on a winding, makeshift network of railways and roads that cross the former Soviet Union.

Those routes carry strategic risks of their own. Access to the transit lines depends on the whims of several authoritarian Central Asian leaders as well as Russian President Vladi­mir Putin, a longtime nemesis of NATO. Moreover, the cost of shipping goods along the northern routes is about triple that of the much-shorter Pakistani lines.

The only other option for departing landlocked Afghanistan is by air — an even more expensive alternative, costing up to 10 times as much as the Pakistani ground routes.

All told, U.S. military logisticians are preparing to bring home 100,000 shipping containers stuffed with materiel and 50,000 wheeled vehicles by the end of 2014, when U.S. and NATO combat operations are scheduled to cease.

The U.S. military has increasingly relied on the supply lines that cross the former Soviet Union to deliver cargo into Afghanistan since those routes opened in 2009.

After Pakistan sealed its border in November to protest a U.S. airstrike that killed 24 of its soldiers, the U.S. military shifted about 60 percent of its supply shipments to the northern routes, with the remainder arriving in the war zone by air. Although delivery disruptions were largely avoided, the move resulted in extra expenses of about $100 million a month.

The importance of the northern routes will become even more acute when the traffic is reversed. By the end of September, 23,000 U.S. troops are scheduled to withdraw from Afghanistan, along with a commensurate amount of materiel.

At first, Russia and several Central Asian countries approved deals that let the Pentagon and NATO deliver “nonlethal” supplies — no ammunition or armored vehicles — into Afghanistan, but provided no mechanism to withdraw the equipment. They also opened their airspace for transport planes carrying troops.

The deals “focused on the needs of entry and didn’t address the needs of exiting,” said Martha Brill Olcott, a Central Asia specialist at the Carnegie Endowment for International Peace. “All of this changed after Pakistan closed down.”

Over the past several months, the Obama administration and NATO have signed two-way transit deals with many of the former Soviet republics. But negotiations continue over a host of side issues, including alternate routes, access to airspace and airports, tariffs and restrictions on what kinds of military cargo are eligible for shipment.