The exercises were agreed after Manmohan Singh, the Indian prime minister, met his Chinese counterpart, Wen Jiabao, on the sidelines of an Asean summit in Singapore last month.
Qin said that although the border issue had still not been resolved despite many rounds of talks, it did not mean China and India could not conduct joint military drills.
"Friendly co-operation between both sides is the main trend. It's natural that there will be disagreements," he said.
"We have disputes over the border issue ... but we will not let it become an obstacle to bilateral relations."
India says China occupies 38,000 square kilometres of its land, while Beijing claims the whole of the northeastern Indian state of Arunachal Pradesh, which is 90,000 square kilometres.