At a public meeting in Doda district, he said the BJP and the PDP tried to build a "structure on sand... Without any foundation. Hence, the building they have built is bound to collapse".
Alluding to the friction in the PDP-BJP ties, he said that the "structure has started crumbling and soon you will witness both the partners biting the dust and moving in opposite direction".
"The PDP-BJP coalition in Jammu and Kashmir is an unholy alliance. It will not survive for long. It can collapse anytime," he said.
The prime minister and the chief minister had on Tuesday discussed steps needed to bring peace back to the Valley, where student protests against police actions have been gaining ground in recent days.
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After the meeting, Mehbooba had said "the coming two- three months are crucial for us" after which a dialogue could be initiated.
The Congress leader alleged that Modi was stirring up the religious sentiments of the people for electoral gains.