The ministry was aware that rumors alleging it was going to drop Project 211 and Project 985 had been doing the rounds at universities, the statement said.
These two projects have effectively promoted the overall quality of China's higher education and there is no plan to abandon them, the statement said.
Project 211 was initiated in 1995 by the ministry for national key universities and colleges, It intended to raise the research standards of targeted universities.
Project 985 was first announced by former Chinese president Jiang Zemin at Peking University's 100th anniversary on May 4, 1998, to promote the development and reputation of the higher education system by founding world-class universities.
China today has over 118 higher education institutions that are designated 211 Project universities and 39 that are 985 Project universities.
Project 211 and 985 universities take on the responsibility of training 80 percent of doctoral students, over 30 percent of graduate students and half of overseas students.
They offer 85 percent of the nation's key subjects, hold 96 percent of the key labs and utilize 70 percent of scientific research funding.