"It is with deep sadness that I condemn the explosions within the hallowed precincts of the most venerated and sacred Bodh Gaya shrine in Bihar in India," the President said in a statement.
"Sri Lanka has undergone similar tragedies when the most venerated and sacred Temple of the Tooth and Sri Maha Bodhi were mercilessly attacked by terrorists, some years ago.
"Therefore, people and the Government of Sri Lanka will extend their fullest support to the people and the Government of India in this hour of great tragedy," he said.
The President's office said he had spoken with the Chief Minister of Bihar, Nitish Kumar, over phone to convey his sadness and condemnation of the terrorist attack.
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Rajapaksa had also spoken to the chief incumbent of the Mahabodhi temple and also directed both the external affairs ministry and the High Commission in Delhi to probe and report to him.
In view of the situation, the pilgrims are warned to delay their departures by one week, the government said.
Nine serial explosions today rocked the temple town of Bodh Gaya in Bihar, including four in the Mahabodhi Temple complex, injuring two monks.
Earlier in the year, the offices of the Mahabodhi Society, the administrative body associated with Bodh Gaya based in Chennai, came under attack by suspected Tamil elements.