Modi made the charge as he broke his silence over cancellation of foreign secretary-level discussions, which had been set for August 25 in Islamabad but were called off after Pakistan's high commissioner to New Delhi met Hurriyat leaders.
"We... were disappointed that Pakistan sought to make a spectacle of these efforts and went ahead with talks with secessionist elements from Jammu and Kashmir," said Modi, according to the Press Trust of India news agency.
But Modi said he would pursue efforts to mend relations between the nuclear-armed neighbours who have fought three wars, two over the disputed Muslim-majority region of Kashmir.
Militant groups have been fighting Indian rule in Kashmir for a quarter-century in a conflict that has claimed tens of thousands of lives, mainly civilians.
"We will continue to make efforts to build peaceful, friendly and cooperative ties with Pakistan," he said.
Modi, who took power in May as head of a new Hindu nationalist right-wing government, was speaking to reporters ahead of a maiden visit to Japan as prime minister.
Pakistan's foreign office had described meetings with Hurriyat leaders as a longstanding and regular practice ahead of talks with India.
Pakistan described the Hurriyat leaders as "stakeholders" in efforts to normalise relations between the two countries, and said the meetings were held "to facilitate meaningful discussions" with India.
Relations between the two neighbours broke down after the Mumbai attacks in 2008, in which 166 people were killed.
Modi's surprise move to invite his Pakistani counterpart, Nawaz Sharif, to his swearing-in ceremony spurred hopes that peace talks between the two countries could resume.
But tensions have been rising between the countries because of several ceasefire violations along the disputed, heavily militarised frontier that each country has blamed on the other.
Modi earlier this month accused Islamabad of waging a "proxy war" by sending militants to attack Indian targets.
He said Friday that India is willing to discuss any "outstanding issue with Pakistan within the bilateral framework", the Press Trust of India reported.
But he insisted that"any meaningful bilateral dialogue necessarily requires an environment that is free from terrorism and violence".
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Free my Kashmir from Indian occupation. Thanks Pakistan for your eternal support. Our prayers are always with you. We are one, and no one can divide us.
Modi means business and is serious to have good neighborly relations with Pakistan. Unfortunately Pakistan is not seen to be acting honestly. It seems the peace between two countries does not suit the main stake holders of Pakistan. Pakistan is neither at peace with itself nor with neighbors. We are proud of Modi and his clear vision to move India ahead in all spheres. India is moving head very fast under Modi. We can feel the "Achche din"
Its time for Pakistan to forget kashmir and concentrate on internal issues , kashmiris want peace, better economy and freedom from Pakistan.