Zhang Chunxian vowed to use “iron fists” on separatists in the region, Xinhua news agency says.
The warning comes on the anniversary of deadly ethnic riots that saw almost 200 people killed in 2009.
Rights group Amnesty International has accused China of intimidating the ethnic Uighur minority.
Xinjiang province is the country’s most westerly region and borders former Soviet states.
China witnessed its worst ethnic violence in decades when riots erupted between the majority Han Chinese and the minority Uighurs in the capital city of Urumqi, says the BBC’s Martin Patience.
The Turkic-speaking Uighurs, who have lived in China’s shadow for centuries, accuse Beijing of religious and political persecution.
Mr Zhang, who is Communist Party secretary of the Xinjiang committee, urged soldiers to remain vigilant against hostile forces and strike separatists, terrorists and extremists with ”iron fists”, Xinhua says.
“We should leave terrorists no place to hide,” he said, adding that the region was stable but faced “severe challenges”.
London-based rights group Amnesty International (AI) issued a statement saying that Chinese authorities “continue to silence those speaking out on abuses” in the region.
