The matter figured in a phone conversation between Pakistan`s Interior Minister Rehman Malik and his Indian counterpart Sushilkumar Shinde.
Malik said he has asked India to provide evidence that elements in Pakistan had used social media networking sites to whip up communal sentiments.
"The Indian minister has said that rumours were generated from Pakistan through cellular services," Malik told reporters referring to his phone conversation with Shinde yesterday.
"I had requested him (Shinde) to provide evidence in this regard to us and we will take care of it," he said.
Malik said he and Shinde discussed the regional situation, including rumours which forced thousands of people from Assam to flee Karnataka, Maharashtra and Tamil Nadu.
Malik had telephoned Shinde to convey greetings for Eid-ul-Fitr and briefly spoke about pending issues between the home and interior ministries of the two countries. This was the first direct contact between them.
Separately, a Foreign Office spokesman dismissed India`s assertion as "baseless and unfounded."
"We totally reject these allegations and insinuations. They are totally baseless and unfounded. Such unsubstantiated statements are not very helpful in creating a conducive environment necessary for improving the relationship between our two countries," he was quoted as saying by The News.
The report said the Indian charge had "irked" Pakistani officials, who claimed New Delhi was again using the media to conduct diplomacy instead of acting in a more responsible manner and sharing information.
The Pakistan Foreign office spokesman said the tools of modern technology were not in the hand of a single person or a national capital, and claimed that the insinuations coming from New Delhi were simply due to people jumping to conclusions, which was not very helpful.
During his conversation with Malik, Shinde had expressed concern over social media networking sites being misused by elements based in Pakistan to circulate false pictures and stories to whip up communal sentiments in India.
Shinde sought Pakistan`s cooperation in neutralising such elements.
On Saturday, Home Secretary R K Singh had said the bulk of the rumours that triggered panic among people of northeastern states in Karnataka, Tamil Nadu and Maharashtra had originated in Pakistan.
After his telephonic conversation with Shinde, Malik said India and Pakistan have expressed their resolve to work for the eradication of terrorism from the region and for the progress of the people of the two countries. "We will have to work jointly for the safety of the region," he said.
Malik said he has invited Shinde to visit Pakistan to take forward work on a revised visa agreement between the two countries.