Kalam died on Monday following cardiac arrest.
The world lost an efficient nuclear scientist with the demise of Kalam, President Hamid said in a message.
Hamid also recalled Kalam's contribution to aeronautical engineering, bdnews24.com reported.
Prime Minister Hasina wrote to her Indian counterpart Narendra Modi late Monday, calling Kalam 'one of the most famous sons of India and a great scientific mind of his time'.
"In president Kalam, we saw the rare combination of a great statesman, an acclaimed scientist and a gifted writer."
"His invaluable contribution to India's rise in the sphere of science and technology would be remembered forever by all," Hasina said in the letter.
She said Kalam took Bangladesh-India relations to a great height when he was the president.
"I am deeply saddened by his death," she said.