The groups banned include the East Turkmanitan Islamic Movement (ETIM), Islamic Movement of Uzbekistan (IMU) and Islamic Jihad Union (IJU).
The ban was introduced on March 15 this year and was first reported by BBC Urdu last evening.
The groups were among the 13 that were banned by then government just before the caretaker set-up came into place including various factions of the Pakistani Taliban, one Sindhi and three Baloch groups.
Chinese authorities and security agencies believed the three organisations were involved in extremist and insurgent activities in the Muslim-majority province of Xinjiang, BBC quoted sources in the Interior Ministry as saying.
Pakistan is reported to have caught and arrested various members of these groups in operations against militants in North Waziristan and other tribal areas. These groups have been the subject of much concern in discussions between the Chinese and Pakistani civilian and military authorities.
Ministry sources were also quoted as saying that Pakistan had been in contact with the Turkish and Uzbek governments over ETIM and IMU, and had learned that over half of the people constituting these bodies were individuals highly wanted by local authorities.
The government has enhanced security of Chinese diplomats in the country against possible attacks by these militants. At least 50-60 organisations already exist on Pakistan's list of banned groups.
Uygurs who constituted over 45 per cent of the province, bordering Pakistan Occupied Kashmir (PoK) and Afghanistan resent the growing settlement of Hans, the majority Chinese race, who now constitute 40 per cent of the population.
China had in 2011 blamed ETIM, believed to be affiliated to al-Qaeda, for violence in the troubled Xinjiang province.
In August 2011, following attacks in which where 20 people, including alleged militants, were killed in violent incidents over two days, China blamed "extremists" trained in terror camps in Pakistan.
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