The February 15 killing of the militant Uighur leader Abdul Haq al-Turkistani by an American drone in the border regions of Pakistan highlighted China’s continued sensitivity when it comes to its remote and vulnerable western region, Xinjiang. It also brought into focus the role of the wider Afghanistan-Pakistan region as an international sanctuary for Islamic militants. This helps to explain the reasons behind Beijing’s worries about social stability and potential terrorist threats in Xinjiang.

China’s neuralgia about security in Xinjiang will continue – and perhaps even grow – as big-power competition for influence and resources in Central Asia and its ties to the rest of the world continue to expand.

China’s troubles with the minority Uighurs are not new. But with the breakup of the Soviet Union two decades ago and the rise of the Islamist Taliban in what was once Soviet-occupied Afghanistan, the region’s dynamics have changed. Since the early 1990s, China has faced recurrent waves of unrest in Xinjiang as well as widespread acts of violence, some of which appear to have been terrorist acts carried out by the disgruntled Uighurs.

The attempted hijacking of an airplane in China in 2008 by three people who were armed with flammable liquid was one of the latest – and also one of the scariest – examples of this trend. There also have been several attacks conducted against perceived Uighur collaborators in China as well as against Chinese interests outside the country. The capture of Uighurs fighting against coalition forces in Afghanistan, some two dozen of whom were imprisoned in the American prison facility at Guantanamo Bay, also indicate that China faces a real threat of terrorist acts directed against its interests both at home and abroad.

The Chinese, however, have aroused skepticism by dubiously attributing dozens of explosions and incidents of civil unrest to instigation by “East Turkistan terrorist forces.” Officials, for example, blamed an August 2008 attack on a military police unit that was out for its morning jog – an incident that led to the killing of 16 officers – on a Uighur terrorist group. However, the fact is that the officers apparently were run down by a truck and were attacked by a taxi driver and a vegetable vendor, which seems hardly to be the modus operandi of a sophisticated terrorist organization.

Even last July’s massive race riot in Urumqi – which were set off by rumors that a Uighur woman had been raped and several Uighur men killed by Han Chinese in far-away Guangdong – was labeled an “organized, violent action against the public” and an act of terrorism.

So, while China does indeed face periodic upsurges in politically motivated violence by Uighurs, one must ask why this is taking place. The answer is that Beijing has, over the decades, engaged in a systematic program of marginalizing Uighurs in their own homeland, as well as fostering economic growth that favors the Han majority of eastern China and that encourages the exploitation of Xinjiang’s wealth of natural resources for Han areas.

Beijing has also organized and encouraged an influx of Han into Xinjiang, changing the ethnic balance that had existed there since 1949 from about 5 percent Han to more than 40 percent today. Moreover, Uighur culture and the Muslim Religion have been placed under tight restrictions. Beijing proudly points out that Xinjiang in recent years has hosted among the fastest growing economies in the country, with per capita income higher than all other regions in China except the country’s southeast coast. Most of that growth, however, has accrued to state-owned enterprises, to Han entrepreneurs, or to the government; not to Uighurs. And income inequalities there have actually expanded significantly in recent years.

The region also suffers from some of the worst environmental degradation that exists in China. It is hardly surprising, therefore, that frustration occasionally boils over into civil unrest – or that such conditions lead to the emergence of terrorist groups intent on taking action against the regime.

That many of China’s problems with terrorism and unrest are largely of its own making has reduced international trust and sympathy for the way Beijing has managed the situation in Xinjiang. China’s concerns also have both shaped its approach to the broader region and reduced China’s willingness to cooperate with the United States on counter-terrorism issues, negatively affecting the overall relationship between the United States and China.

Xinjiang, more than any other area of China, is strategically vulnerable. This is partially as a result of its location in one of the most fractious neighborhoods in the world outside the Middle East. Representing one-sixth of China’s territory, Xinjiang is rich in oil, gas, and mineral deposits. The region also contains numerous sensitive Chinese military installations, including some of the country’s premier nuclear research and testing facilities. It borders the former Soviet republics of Kazakhstan, Kyrgyzstan, and Tajikistan, all of which are less than politically stable. (Beijing is some 2,400 kilometers from Xinjiang’s capital, Urumqi; Urumqi is around another 1,100 kilometers from Kashgar on the far Western border. By contrast, Kashgar is only 400 kilometers from Bishkek, Kyrgyzstan and some 800 kilometers from the capital of Afghanistan, Kabul.)

Complicating China’s relations with the Central Asian states is the fact that as many as 500,000 Uighurs – and sizable populations of other Chinese “minorities” – live across relatively porous borders and engage in extensive trade and contacts. Several of these countries contain anti-China Uighur separatist organizations, some of them peaceful, others terrorist.

And China is very afraid of the potential contagion of “color revolutions” from Central Asia – like the 2005 “Tulip Revolution” in Kyrgyzstan – that could destabilize China’s control over Xinjiang.

Uighur activities – including violent attacks – have also complicated China’s relations with Turkey, a country with which China seeks closer relations but where public and official sentiment has also been highly critical of China’s treatment of the ethnically-related Uighurs.

To control this potentially chaotic situation and to manage Sino-Russian competition for influence, China launched the Shanghai Cooperation Organization, which includes Russia, China, the Central Asian republics, and a growing number of observers from around the region. China has pushed hard to keep the focus of the organization on cooperative activities against the “three evils” of “separatism, fundamentalism, and terrorism.” These are fears that all of the member states have in common.

Along some of Xinjiang’s most remote and sensitive borders are Tibet, Afghanistan, Pakistan, and the disputed region of Kashmir. The outbreak of violence in any one of these areas could quickly embroil China in an international crisis. China has also tested its “all-weather” friendship with Pakistan by pressuring Islamabad to crack down on Uighur militants who have sought refuge in Pakistan. Islamabad reportedly has responded by sending a number of the Uighur militants back to China for prosecution. Its recent decision to step up attacks against terrorist groups – and especially the killing of Abdel-Haq and more than a dozen other Uighur militants – has, among other things, helped improve Pakistani relations with China.

The military intervention of the United States in Afghanistan in October 2001 introduced another variable of vulnerability for China with regard to Xinjiang. In the conflict that followed, global support for Al-Qaeda drew in more militants to the region, including some Uighurs (as Abdel-Haq’s death proved). However, it also changed the strategic landscape for China. The introduction of massive numbers of American forces into the region, and especially the use of bases such as Manas in Kyrgyzstan, provoked visceral and long-standing Chinese fears of encirclement by a hostile United States that is intent on “dividing and Westernizing” China.

As a consequence of this fear, Beijing has put pressure on its Central Asian neighbors to expel or to severely limit the scope of the American military presence in their countries. Beijing has also refused to allow American forces to use Chinese territory for staging operations or for overflights in the ongoing war in Afghanistan. China is also working hard to enhance cooperation with its neighbors on energy exploration, exploitation, and transportation as a way of keeping the United States and Russia from monopolizing Central Asia’s voluminous oil and natural gas resources.

These competing interests, and the residual worry that the United States and Russia are seeking to supplant or minimize Chinese influence in Central Asia will continue to contribute to Beijing’s sensitivities about assuring stability in its far Western extremity, even if the real terrorist threat to China has actually diminished.

Christopher M. Clarke is an independent China consultant. He retired in 2009 after 25 years as a China analyst and as the head of the China Division of the State Department’s Bureau of Intelligence and Research. This commentary is reprinted with permission from YaleGlobal Online (www.yaleglobal.yale.edu). Copyright © 2010, Yale Center for the Study of Globalization, Yale University.