Yang Jiechi discussed the subject during a trip to Islamabad, where he met with Pakistani President Asif Ali Zardari.
The people in question belong to the East Turkestan Islamic Movement, a militant group that is fighting to free the Muslim-dominated Xinjiang province from Chinese rule.
ETIM, which has been designated a terrorist organization by the U.S. and U.N., has reportedly operated military training camps in both Pakistan and Afghanistan since the mid-1990s.
Pakistani intelligence networks have also been feeding information about the Uighur militants on their soil to their counterparts in Beijing.
Ethnic violence in the Xinjiang province in far western China has killed hundreds of people since the outbreak of disturbances three years ago. Beijing has blamed ETIM for the unrest in Xinjiang and has also linked them to al-Qaeda.
However, up until now, China did not want to embarrass Pakistan, an important regional ally and bulwark against South Asian giant India, by explicitly suggesting that the Pakistanis were knowingly harboring Uighur militants.
According to the U.S. State Department, most Uighurs do not support the independence movement and there are questions surrounding how large and dangerous the ETIM really is.
Uighurs, who are racially and religiously distinct from the Chinese, now account for only about 45 percent of Xinjiang’s population, and that figure keeps declining due to large-scale immigration of the dominant Han Chinese into the region.
Xinjiang also possesses huge oil reserves and is also China’s biggest natural gas-producing area.