By Rayhan Demytrie
BBC Central Asian correspondent
Kyrgyzstan said the US had not paid enough rent for the Manas air base
Tajikistan and the US have finalised a transit deal for the shipment of non-military supplies to Afghanistan.
The first shipments - by road and rail - should pass through Tajik territory in a matter of weeks.
US Assistant Secretary of State Richard Boucher, who is on a visit to the region, said the negotiations had concluded satisfactorily.
The deal follows a decision by Kyrgyzstan to close a US air base - the only US military base in Central Asia.
Washington has been seeking ways to transport non-military supplies for US and Nato forces in Afghanistan via several Central Asian states as alternatives to the existing Pakistan route.
So far, most countries have given their consent.
US Rear Admiral Mark Harnitchek said in February that, with approval from Tajikistan, 50 to 200 containers could be transported every week by road and rail from Uzbekistan to Tajikistan and then into Afghanistan.
Previously, the US has used its military supply air base at Manas in the republic of Kyrgyzstan.
But the authorities there terminated an agreement with Washington in February giving the US military six months to leave.
Mr Boucher said: "We are not particularly looking for some other base in the region. We can conduct these operations elsewhere."
He added that the new US administration under President Barack Obama wanted to "continue and expand our involvement in relations with Central Asia".
"We want to work closely with this region. Together we can help bring stability to Afghanistan," he said.
EXISTING/POSSIBLE SUPPLY ROUTES TO TROOPS IN AFGHANISTAN
1. Manas airbase:
The only US base in Central Asia, a vital transit point for Nato and US operations. Kyrgyz government has given notice of its closure
2. Karshi-Khanabad airbase:
US forces were ordered out in 2005. Uzbekistan may agree to allow it to be used for non-military transports
3. Bridge over Panj river:
part-funded by the US, it was completed in 2007. May serve as another supply route into Afghanistan
4. Khyber Pass:
most supplies to US and Nato troops come through Pakistan. Increasing number of attacks in the area mean the US army is looking for back-up routes