It contradicts US statements that talks are ongoing about the base’s future.
Meanwhile, the US has asked to move supplies through Russia, and Tajikistan has said it will allow the transit of non-military goods into Afghanistan.
Nato is understood to be increasingly concerned about the security of its supply routes through Pakistan.
Most of its supplies come through Pakistan’s Khyber Pass, which has come under increasing militant attacks.
“The decision has been made,” said Kyrgyz government spokesman Aibek Sultangaziyev.
“The US embassy and the [Kyrgyz] foreign ministry are exchanging opinions on this, but there are no discussions on keeping the base.”
See map of existing and possible supply routes in the region
Manas, just outside the capital Bishkek, is the only US base in Central Asia and is a vital transit point for Nato and US operations in Afghanistan – an hour-and-a-half’s flight away.
The base is used to refuel Afghan-bound planes, and is the first point of stop for the majority of coalition troops on their way in and out of Afghanistan.
The closure announcement came after Russia promised Kyrgyzstan $2bn (£1.4bn) in aid. However, Kyrgyzstan says the moves are not linked.
Kyrgyz MPs will vote on the closure later this month.
Russia has long opposed the presence of American military forces in Central Asia, says the BBC’s Richard Galpin in Moscow.
Russia says it has agreed to a request from the US to allow the transit of non-military Nato supplies across its soil, but says it is waiting for details of specific shipments before issuing permissions.
“As soon as that happens we will give the corresponding permission,” said Foreign Minister Sergei Lavrov, quoted by Russian media.
For the US, the base closure comes at a critical moment, as the new administration of President Barack Obama plans a sharp increase in the number of American troops in Afghanistan.
For Russia, on the other hand, its closure would be a significant diplomatic victory as it seeks to reassert its influence in all former Soviet republics and beyond, analysts say.
The Manas base was set up in 2001 to assist the US military operation against al-Qaeda and the Taleban in Afghanistan.
Under the lease agreement, the US must be given six months’ notice to close its operations.
Meanwhile, diplomatic sources say that the US is close to a deal with Uzbekistan as part of back-up plan.
The US left its air base there following a dispute over human rights in 2005. BBC