Kurmanbek Bakiyev, the president of Kyrgyzstan, signed a bill to close the base in February, giving the US six months to shut it down.
The Kyrgyz parliament passed the bill a month after Russia offered the country $2.15bn in aid and loans for its weak economy.
Russia operates its own air base in Kyrgyzstan, but both nations said the closure of the US base was not a condition of the Russian aid.
Bakiyev complained at the time that the US was not paying enough in rent for the base.
US officials have expressed hope that Kyrgyzstan could change its mind, indicating that negotiations on the amount paid for its maintenance could be held.
Hamid Karzai, the president of Afghanistan, has also appealed to Kyrgyz officials to continue to allow coalition troops to use the base.
The base is used as a transit point for 15,000 troops and 500 tonnes of cargo monthly to and from Afghanistan.
The US pays $17.4m annually for the base, which was opened just after its offensive in Afghanistan began in 2001, following the September 11 attacks.
Closure of the Manas base would remove the last US air base from central Asia.
The US has said Tajikistan and Uzbekistan will allow the transit of non-military Nato cargo by road and rail to Afghanistan to supply troops.