Expressing deep anguish over the blasts, President Mukherjee said it was a "senseless act of violence targeting innocent pilgrims and monks who had gathered to worship at this temple dedicated to the great apostle of peace -- Gautam Buddha".
In a statement, the President hoped for the speedy recovery of those injured in the blasts.
Asking people to maintain calm and restraint, he asked them to cooperate with the authorities in bringing the perpetrators to justice.
Nine serial explosions rocked the internationally renowned temple town of Bodh Gaya, including four in the Mahabodhi temple complex, injuring two monks in the blasts.
The Mahabodhi temple is frequented by Buddhist pilgrims from Sri Lanka, China and Japan and the whole of southeast Asia.
Tibetan spiritual leader the Dalai Lama makes frequent trips to Bodh Gaya and Sri Lankan President Mahinda Rajapaksa had visited it six months back. A total of 52 countries have established their monasteries here.
Strongly condemning the terror strike on the Mahabodhi temple in Bodh Gaya, Prime Minister Singh said such attacks on religious places will "never be tolerated".
"The prime minister has strongly condemned the blasts in around the sacred Mahabodhi temple at Bodh Gaya. He has said that our composite culture and traditions teach us respect for all religions and such attacks on religious places will never be tolerated," a release from the Prime Minister's Office said.
The prime minister also wished speedy recovery to the people injured in the attack.
Nine serial blasts took place inside and outside the Mahabodhi temple in Bodh Gaya early on Sunday in which two monks were injured.
Image: President Pranab Mukherjee