"If somebody makes such a statement, we can never support it," Modi said in Rajya Sabha, referring to the controversial remarks made by Sayeed who is heading a PDP-BJP coalition government in the state.
Members have been demanding Modi's response to the remarks made by Sayeed soon after he was sworn-in on Sunday.
"If somebody makes a statement somewhere and we are forced to respond here, things will not work," the Prime Minister said.
Modi said the credit for the successful elections goes to the people of Jammu and Kashmir who "removed doubts" in the international community by turning up in large numbers with "overwhelming courage and pride" and "put their stamp of approval on what India had been saying all along".
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He underlined faith in people of Jammu and Kashmir while asserting his government's commitment to unity and integrity.
On questions by some members whether BJP will pull out of the coalition government over the issue, Modi said the government will run only on the basis of Common Minimum Programme (CMP).