But lately, it seems it's getting even harder.
In Uzbekistan, the government has withdrawn the registration of some foreign NGOs and openly criticized the work of others. It's an attitude that seems to be contagious across the region.
David Lewis works in Kyrgyzstan for the International Crisis Group, a U.S.-based NGO.
"Unfortunately, of course, in several countries in Central Asia there's considerable pressure on [NGOs], particularly in Uzbekistan and Turkmenistan. And they often operate under difficult restrictions. There's a fairly wide spectrum of NGOs and often those subjects have a certain political element to them inevitably, which is why they often face some problems from the authorities," Lewis said.
Ian Bremmer is president of the U.S.-based Eurasia Group. He says the political nature of NGO work in Central Asia is clear when compared with their role in Afghanistan.
"It [NGO work in Central Asia] is, in a sense, far more politicized. We are not talking about nearly as much reconstruction, which is the focus in Afghanistan. In Central Asia we're talking much more about problems with openness, the media, political reforms, helping to create a civil society," Bremmer said.
Given the nature of governments in Central Asia, some might wonder why they allow foreign NGOs to work there at all.
Turkmenistan, in fact, is an exception. Ashgabat allows only a few such groups to work on Turkmen territory. And none have anything to do with politics.
But the region's other countries have been more tolerant. Bremmer explains why many foreign NGOs were originally allowed to operate.
"These organizations were allowed to be formed in the beginning because they were felt to be part of a package that had to be accepted to gain the interest and the willingness to deal with these countries of the West. They didn't want to be ostracized like, say, a Belarus or Turkmenistan," Bremmer said.
Now, however, things appear to be changing. Because of the region's wealth in hydrocarbon resources and its strategic location, Bremmer says Central Asian governments no longer feel the need to endure criticism from these NGOs and their perceived meddling in internal affairs.
He says that these governments now believe that the West will not abandon the region purely as a protest at the lack of human rights and freedom.
Earlier this week, authorities in Uzbekistan temporarily suspended Internews, an international media organization. Uzbekistan's Justice Ministry said the organization had failed to register its logo, inform the ministry about activities outside the capital, accurate number of board members and a change of address.
Alex Lupis works for the Committee to Protect Journalists as the senior program coordinator for Europe and Central Asia.
"Internews works on two fronts. On one front, they're training radio and television journalists and clearly their work is having an impact by helping the independent broadcast media be more professional, more effective in Uzbekistan and that is definitely a threat to the government because they feel like the media might not be as politically subservient as it had in the past. Secondly, Internews has also been doing an incredibly wonderful job documenting press freedom abuses by the government in Uzbekistan," Lupis said.
In another recent case, the New York-based Soros Foundation's Open Society Institute (OSI) was denied registration in Uzbekistan. The Uzbek Justice Ministry said the organization was guilty of "crude breaches of the law."
The Uzbek government has also recently warned other NGOs about their activities.
Ulughbek Ismailov, head of Uzbekistan's State Agency on Media and Information in the western Khorezm Province, recently voiced his feelings about foreign NGOs.
"If they [NGOs] want to open a private television or radio station or a newspaper they are welcome, but they need to present the documents required by law. Then they can work freely. But if they want to get involved in government politics, their newspaper or television station is going to get politicized. I think they need to stay away from politics and just give interesting information," Ismailov said.
Analysts say governments are growing impatient with foreign NGOs that help opposition parties and the media to publicize the shortcomings of officials.
Although Uzbekistan has parliamentary elections in late December, the Justice Ministry has yet to register any genuine opposition parties.
In Tajikistan, Soros' OSI is facing problems less than six months ahead of parliamentary elections. The chairwoman of the organization in Tajikistan, Oynihol Bobonazarova, says the trouble just started.
"Up until 14 September, we didn't feel pressure from either the government or the state media. But all of the sudden all the government newspapers printed baseless articles that has forced us to re-evaluate our situation," Bobonazarova said.
Such articles have included accusations that the OSI in Tajikistan is corrupt.
Lupis of the CPJ says Central Asian governments might be worried about a repeat of the events in Georgia last November, when the so-called Rose Revolution toppled the regime.
"There is some sensitivity to what happened in Georgia at the end of 2003 where independent media and NGOs did play quite an influential role in ousting Georgia's authoritarian and corrupt leader Eduard Shevardnadze out of office," Lupis said.
The Russian newspaper "Kommersant" has reported that during a speech earlier this week in Moscow, Kyrgyz President Askar Akaev referred to the events in Georgia.
He says tactics used in the Rose Revolution are now being aimed at weakening governments in the Commonwealth of Independent States.
(The Tajik and Uzbek services contributed to this report)