U.S. Defense Secretary Robert Gates said, however, that he believed the base was not a "closed issue." The U.S. has said it would consider paying more rent to keep the base open.
He also said he wasin Kyrgyzstan's decision.
Pakistani militants have stepped up attacks on convoys traveling the primary supply route to Afghanistan in recent months pushing U.S. officials to secure alternative, northern routes through Central Asia.
The U.S. announced a small victory in that hunt Friday saying neighboring Uzbekistan had granted permission for the transit of non-lethal cargo to Afghanistan.
"I continue to believe this is not a closed issue, and that there remains the potential to reopen this issue," Gates said when asked about the closure of the Manas base. "But we are developing alternative methods of getting resupply and people into Afghanistan."
Washington has received Russian permission for non-lethal cargo to be shipped across Russia. Central Asia's largest country, Kazakhstan, has also agreed.
But there's been uncertainty about how cargo would get across former Soviet Central Asia, particularly given uneasy relations between Washington and the country straddling the easiest route into Afghanistan Uzbekistan, one of the most politically repressive of the former Soviet states.
Most of President Islam Karimov's opponents have been sent to jail or into exile. U.S.-based Human Rights Watch has said that Uzbek prison authorities routinely abuse and torture prisoners.
Anger over Western criticism of a crackdown on an uprising in eastern Uzbekistan prompted the government to evict U.S. troops from an air base near the Afghan border in 2005, leaving the Manas air base in Kyrgyzstan as the only U.S. base in Central Asia.
The Kyrgyz move to close Manas a transit point for 15,000 troops and 500 tons of cargo each month heading to Afghanistan caught the United States by surprise.
Kyrgyzstan's president complained when announcing the closure this month that the United States was not paying enough rent for the base. The announcement came shortly after Russia said it would give $2.15 billion in aid and loans to the impoverished Central Asian nation. U.S. officials suspect that Russia, long wary of U.S. presence in ex-Soviet Central Asia, is behind the decision to shut the Americans out. The U.S. has complained of mixed messages from Russian on Moscow's willingness to help with the Afghan war effort.
The U.S. Embassy in Bishkek confirmed Friday that it had received formal notification of eviction from the Kyrgyz Foreign Ministry, but had no further comment.
The commander of U.S. operations in Afghanistan and Iraq, Gen. David Petraeus, traveled to the Uzbek capital, Tashkent, earlier this week to meet with Karimov. No details of his visit were released.
But on Friday, U.S. Rear Admiral Mark Harnitchek a military transportation officer said that Uzbekistan had reached a deal for cargo to be shipped across its territory.
"We have a tentative agreement with Uzbekistan on transit," he said during a visit to another Central Asian nation that borders Afghanistan, Tajikistan. His comments were shown on Tajik state television.
Some of the goods will be transported from Uzbekistan onward through Tajikistan, which also shares a direct border with Afghanistan, Harnitchek said.
"We plan to move between 50 and 200 containers to Afghanistan through Tajikistan every week," he said.
It was unclear why the cargo would not be shipped directly from Uzbekistan into Afghanistan. U.S. Embassy officials in Uzbekistan declined to comment, as did the Uzbek Foreign Ministry. U.S. Central Command officials could not be immediately located for comment.
President Barack Obama announced earlier this week that he would send 17,000 more U.S. troops to Afghanistan to augment the 33,000 already there.