"The Government of Pakistan expresses its condolences on the demise of Dr A P J Abdul Kalam, former President of the Republic of India," the Foreign Office said.
"Dr Kalam will be remembered for his meritorious services for his country," it said in a statement.
Kalam, 83, also known as India's 'missile man', collapsed during a lecture at the Indian Institute of Management in Shillong this evening and later died in a hospital.
Kalam served as the President of India from 2002 to 2007.