Putin said in a joint press conference with Atambaev after the meeting that the Russian base in Kyrgyzstan and Russian bases in neighboring Tajikistan are "acting as a factor of stability" in those two countries and in Central Asia generally.
"[The Russian military base in Kyrgyzstan] was established after gangs of terrorists had entered the territory of Kyrgyzstan and when the leadership of Kyrgyzstan requested Russia to set up a military outpost here that would stop the flow of drugs and extremism into Kyrgyzstan," Putin said. "We did it back then, and now we have agreed on its further functioning."
Just ahead of Putin's arrival in Kyrgyzstan, Russian media reported an agreement on Russian use of the Kant military base, some 40 kilometers from Bishkek, was ready for signing. Those reports said rent for use of the base would remain $4.5 million annually, as it has been since 2003 when the original agreement was signed.
Atambaev said after the talks that cooperation with "the great nation of Russia" is crucial for his nation.
During the meeting, the two presidents signed a document confirming Russia will gradually write off Kyrgyzstan's entire $489 million debt by March 2016. Russia had already said it would simply cancel $189 million of that debt and acquire shares in Kyrgyz industries, including the torpedo factory at Kyrgyzstan's Issyk-Kul.
The subject of a U.S. base in Kyrgyzstan came up at the two presidents' press conference.
Atambaev said the U.S. base at Manas, which is being used as a transit center to ferry supplies and troops to Afghanistan, would be closed.
A joint statement signed by Putin and Atambaev mentioned "Kyrgyzstan's intention to transform the transit center at Manas airport…into a civilian facility free of any military component" after the U.S. lease expires in 2014.
Putin and Atambaev also agreed Russian companies would help complete a network of hydropower plants in Kyrgyzstan that were started during Soviet times.
The ministers of energy signed agreements to finish construction of the Naryn Cascade project and Kambar-Ata-1, but Putin said there was no specific date for that work to start.
"I want to emphasize that these are large, serious, multibillion [ruble] projects that will help develop [Kyrgyzstan's] economy, create new jobs, and improve the well-being of Kyrgyz citizens," Putin said.
He added that Kazakhstan and Uzbekistan -- two countries that have expressed concerns about the effects of Kyrgyz hydropower plants on their agricultural lands -- could join in the projects, which the Russian leader assured would not have any adverse consequences for farming in those neighboring countries.
Putin also pledged to help Kyrgyzstan's entry into the CIS Customs Union that groups Russia, Kazakhstan, and Belarus, and also the Common Economic Space.