The ruling Communist Party's anti-graft watchdog said in a brief statement National Energy Administration Director Nur Bekri was being probed on suspicion of breaking the law and violating party discipline, the usual euphemism for graft but which could also refer to other legal problems.
It gave no other details and it was not possible to reach Nur Bekri for comment.
President Xi Jinping has targeted the energy sector as part of a wider war against pervasive graft that began when he came into office six years ago.
Nur Bekri, 57, worked in Xinjiang until moving to Beijing in late 2014 to head the energy administration. He is also a deputy head of China's powerful state planning agency, the National Development and Reform Commission.
He is one of the few Uighurs - a Muslim people who speak a Turkic language and who call Xinjiang home - ever to have broken through and made it to a top national-level job in Beijing.
Xinjiang has been one of China's most violent regions, with hundreds killed in unrest between the minority Uighurs and the majority Han Chinese in recent years.
Nur Bekri was Xinjiang's governor from 2008 until 2014, a time that saw bouts of ethnic violence that included deadly rioting in the region's capital, Urumqi, in 2009.
During his time in that position, which ranks below the Communist Party secretary, Nur Bekri was a proponent of restrictions placed on religious practices of the largely Muslim ethnic minorities there, ostensibly to curb what the government said was the spread of extremist ideology.
He said in the wake of the 2009 riots the government's religious policies completely accorded with the interests of the people.
Nur Bekri had also touted bilingual education for Uighurs in schools as a route to economic opportunity, although critics said in reality that meant marginalizing the Uighurs' own language and culture in favor of Mandarin.
Ilham Tohti, a Uighur economics professor and outspoken critic of Beijing's policies towards his people, was jailed for life on separatism charges in 2014, a sentence that caused an outcry from human rights advocates. Nur Bekri called the evidence against him irrefutable before he was jailed.
Nur Bekri's tenure as governor ended under then party secretary Zhang Chunxian, who was replaced as Xinjiang's chief by Chen Quanguo in 2016.
Chen dramatically ramped up police presence and mass surveillance on minorities compared to his predecessor, and ushered in the use of mass detention centers that has sparked a growing international outcry in recent months.
China denies the abuses and says the "vocational"-style training centers, thought to hold potentially a million Uighurs and other Muslims, were designed to prevent extremism.
Calls are growing from Western countries for action on the camps and U.S. officials have said they were considering sanctions on Chinese officials and companies linked to the crackdown.
(Reporting by Andrew Galbraith and John Ruwitch in SHANGHAI, and Michael Martina and Christian Shepherd in BEIJING; Editing by Paul Tait)