The military presence is accompanied by a package of economic incentives, allowing Tajikistan to repay its Russian debts while receiving large Russian investments in its main industries.
Alex Vatanka of "Jane's Defence Weekly" said this coupling of military and economic support is increasingly a new Russian approach.
"This is not just going on in Tajikistan," Vatanka said. "You have seen similar scenarios in Armenia; you have seen it being shaped and promoted in Azerbaijan; you have seen it in the past in Georgia; you see it heavily in Ukraine; you have seen it recently in Uzbekistan."
Tajikistan, because of its position between Afghanistan and China, is considered strategically important.
Putin is well aware of the fact that U.S. and NATO-led troops are in the northern areas of Afghanistan, in close proximity to the Tajik border. He is also aware of NATO plans for further military cooperation in Central Asia.
NATO Secretary-General Jaap de Hoop Scheffer, who is on a tour of the Central Asian republics, reaffirmed the importance of cooperation between NATO forces in Afghanistan with Central Asia.
"I am confident that very soon indeed [NATO] can come to an agreement with a number of nations in the Central Asian region, to agree on the so called 'Lines of Communication Agreement' so that NATO's [operation] in Afghanistan -- which will expand to the west of the country -- can be supported through the region as well," de Hoop Scheffer said.
Vatanka said Russia is unhappy with the increasing U.S. and NATO presence.
"Russians are very, very apprehensive about American presence in Central Asia. What they want to see is a gradual withdrawal of all American troops from Central Asia. But you know that won't come, and Russians know that, and I think that's exactly why they are committing more and more resources."
In the aftermath of the 11 September 2001 attacks, the Tajik president, like some of his counterparts in Central Asia, indicated a growing preference for relations with the West.
Tajik President Imomali Rakhmonov was supportive of the U.S.-led "war on terror" and cooperated by allowing military flights from Tajikistan. As a sign of pushing Russia back, he asserted openly that it was time for Russian troops to leave the Tajik-Afghan border and requested that a detachment of Russian troops - dating from Soviet times -- be moved to a less prominent location in the Tajik capital Dushanbe.
Now, Putin's strategy appears to have won the day. The new Russian base in Dushanbe will house 5,000 soldiers and could be expanded to an air base in future. At the same time, Russia will write off $330 billion of Tajik debts and says it will provide investment amounting to $ 2 billion over the next five years.
Putin said in the past 12 years no country had equaled such a generous investment in Tajikistan. However, he omitted to say Russia is also planning to own the two main industries of Tajikistan, namely the hydropower plant at Sangtudeh and the new aluminum plant in Khatlon region. Details on these are sketchy and officials have declined to give information on them, but there has been talk of over 50 percent Russian share in both these industrial plants.
Tajik reaction has been mixed, some welcoming the Russian moves as a positive step toward better security and more economic prosperity. Others, such as Dadejan Attaullah, a well-known Tajik opposition figure, say Tajikistan has been sold to Russia, arguing that if in the old days Tajik dependence on Russia was mainly political, it has now become political, economic and military.
"Yesterday, after a couple of years of discussions, separation and stone throwing, finally Tajikistan was fully and completely sold off to Russia," Attaullah said.
The Russian newspaper "Nezavisimaya gazeta," commenting on Putin's visit that Russia had finally managed to achieve a cherished aim -- a military base in Tajikistan. Moscow is investing substantial sums in the country's economy, while at the same time "greatly increasing its military presence in Central Asia."