Igor Chudinov, the Kyrgyz prime minister, said his country was "in the process of negotiations with the Americans" and denied that the move to close the base was linked to Russia's aid package.
"Talks on Russian aid have been going on for two years, and they were in no way related to the issue of the removal of the air base from Kyrgyzstan," he said.
Bryan Whitman, a Pentagon spokesman, said the base was "something that the US government continues to discuss with Kyrgyzstan officials. We're still very much engaged on this issue".
He also said it was unlikely Russia was attempting to undermine US presence in the region.
"It certainly doesn't make any sense for Russia or any other country in the region to try to undermine the international effort to bring stability to Central Asia," he said.
"They [Russia] have been very consistent in their public statements in the past about supporting the international effort to bring stability in Afghanistan as well as the region."
Kyrgyzstan has expressed unhappiness over the prolonged presence of the base.
"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," Bakiyev on Wednesday.
The original deal between the US and Kyrgyzstan gives Washington six months to shut down the base after being informed of its closure by the government.
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 military focus away from Iraq.