The base in Manas, outside the capital Bishkek, had been set up to assist international forces in Afghanistan but Kyrgyzstan has been unhappy over its prolonged presence.
Bakiyev said: "The problems that have amassed stir up a negative response in our society and people justly raised the question, and have been doing so for quite a while, about the reasons to have the base on the territory of Kyrgyzstan.
"Literally the other day, the government of Kyrgyzstan made a decision on ending the term for the American military base on the territory of Kyrgyzstan."
The US embassy in Kyrgyzstan said that it had not received any notification on the decision and that talks were still under way.
"Discussions will continue," the embassy said in a statement.
"We have a broad range of programmes and interests we will continue to pursue with the government and people of Kyrgyzstan."
Speaking on Wednesday, Medvedev said: "Russia and other [ex-Soviet allies] are ready for full-fledged comprehensive co-operation with the United States and other coalition members in fighting terrorism in the region.
"This fight must be comprehensive and include both military and political components. Only in the case will this have a chance to succeed".
It was not clear if Medvedev's reference to "full-fledged" co-operation was an attempt to reassure Washington or an indication that Moscow would seek concessions in exchange for helping to keep the air base open.
In a statement, the Kyrgyz government said: "Eight years has passed since the agreement was signed. Over that period the threat that existed has been removed.
"This is one of the fundamental reasons for the cancellation of the agreement."
The original deal by the US and Kyrgyzstan gave Washington six months to shut down the base after being informed of its closure by the government.
Al Jazeera's Nazanine Moshiri said: "It [the base] is highly important to US forces' plans to double troop numbers in Afghanistan and key to seeking alternative supply routes that bypass Pakistan, where there is significant security risk.
"If the go ahead is given the US will have 180 days to leave. The runway that was built for Soviet bombers could soon be back in the hands of its orginial owners".
About 30,000 more US soldiers are expected to be sent to Afghanistan in 2009 as the administration of Barack Obama, the US president, plans to shift its foreign policy focus away from Iraq.