ISRO Chairman A S Kiran Kumar received the honour which carries Rs one crore in cash, a plaque and a citation.
"Countering the challenges of scarce resources, limited technical manpower and physical infrastructure in the early years, ISRO has today established operational space systems and services, attained self-reliance in development of indigenous technology and accomplished exemplary feats in space exploration.
"It has, at the same time, remained true to its mission of bringing space to the service of the common man," the President said.
Mukherjee praised ISRO for scripting space history on September 24, 2014 by successfully placing the Mars Orbiter around Mars. India is the only country in the world to achieve this feat in its first attempt and ISRO the fourth space agency in the world to reach Mars.
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ISRO's people centric space programmes are designed to support various national priorities such as food and water security, sustainable environmental practices, conservation of resources, livelihood support, poverty alleviation, rural prosperity, education and health care and disaster management amongst others, the President said.
Gandhi Peace Prize, whose secretariat is provided by Culture Ministry, is presented annually by the President. This award is given to individuals and institutions for their contribution towards social, economic and political transformation through non-violence and other Gandhian method.
Vice President Hamid Ansari, Prime Minister Narendra Modi, Culture Minister Mahesh Sharma, Minister of State in Prime Minister's Office Jitendra Singh and senior BJP leader L K Advani and other dignitaries were present in the ceremony.