"Congratulations to @isro on being conferred the Gandhi Peace Prize," he tweeted, hours after the space agency was presented the award by President Pranab Mukherjee here.
"This is a fitting tribute to the hardwork of generations of scientists," Modi added.
ISRO was given the prize in recognition of its services in transforming India through the use of space technology and space based services.
ISRO Chairman A S Kiran Kumar received the honour which carries Rs one crore in cash, a plaque and a citation.
"It has, at the same time, remained true to its mission of bringing space to the service of the common man," the President said.