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.

“These countries know it’s the last chance, it’s the last negotiation, so they’re going to squeeze very hard,” said Alexander Cooley, a Barnard College professor and expert on U.S. military relations in Central Asia. “They can escalate their demands in the confidence that this is a one-off transaction.”

Even with Pakistan reopening its border, the northern routes are seen as a vital hedge against a Pakistani change of heart.

From Afghanistan’s north, there are two primary ways out: either by rail into Uzbekistan or by road into Tajikistan. Both are authoritarian countries with checkered human rights records.

Beyond that, shipping convoys — which are run by private companies — must cross Kazakhstan or Kyrgyzstan, with most of the land routes then entering Russia before zigzagging to ports in Siberia or on the Baltic Sea.

Negotiating with the Central Asians has often been as difficult as with Pakistan, according to U.S. and NATO officials. The countries distrust, compete with and often try to sabotage each other while simultaneously seeking to exact more concessions from Washington and its allies.

“They all want to play against each other,” said a senior NATO official, speaking on the condition of anonymity to discuss the negotiations.

NATO Secretary General Anders Fogh Rasmussen announced last month that the alliance had forged agreements with Kazakhstan, Kyrgyzstan and Uzbekistan to allow for the withdrawal of equipment from Afghanistan.

A NATO spokeswoman declined to release details of the accords, such as transit fees, but acknowledged that weapons and ammunition are still prohibited cargo on the northern land routes.

NATO remains in talks with Russia about establishing an air hub in the city of Ulyanovsk — Lenin’s birthplace — that would accept rail shipments from Central Asia and then load the containers onto Europe-bound cargo planes.

Vice Adm. Mark D. Harnitchek, a senior U.S. military logistician who was instrumental in setting up the northern routes, said he was confident the network would remain reliable during the withdrawal.

“If you were going to design a system to come into Afghanistan, you wouldn’t do it from the north, but it’s proven to be robust,” Harnitchek, director of the Defense Logistics Agency, told reporters last week. “Those countries have all been remarkably cooperative.”

But many haven’t hesitated to exploit their bargaining power to make special demands.

In April, for example, military officials from Kyrgyzstan asked Marine Gen. James Mattis, the head of the U.S. Central Command, whether the Pentagon would be willing to donate drones after its departure from Afghanistan. Mattis was noncommittal, saying he would forward the request to Washington, according to a report of the encounter by Radio Free Europe.

Meanwhile, Uzbekistan has sought to capi­tal­ize on its status as the only country with a major rail link to Afghanistan by seeking a 50 percent surcharge on shipments leaving the war zone — insisting on a premium over what its neighbors earn.

“Everybody wants to up the prices,” Olcott said. “The Kazakhs complain that the Uzbeks get much better terms.”

She said the same regional rivalries have emerged when Washington has sought to compensate countries with used military equipment instead of cash.

“The Uzbeks complain about the Tajiks, or the Kazakhs about Kyrgyzstan, that it will just give them weapons they can effectively use against their neighbors, or against trouble in their own country.”