Union Home Secretary R.K. Singh told The Times of India newspaper that the government believes most of the incendiary videos of atrocities allegedly committed on Muslims in the state of Assam as well as in Myanmar came from Pakistan.
"Technical investigation has established that a bulk of the incendiary images was first uploaded on blogs in Pakistan," he said.
He said the object was to incite inter-ethnic violence within India and New Delhi will be raising the issue with Pakistani officials.
"I am sure they (Pakistan) will deny it but we have fairly accurate technical evidence to show that the images originated and were circulated from their territory," he said.
"As many as 110 Web sites were involved in spreading the doctored clips. We have blocked 76 of them and are in the process of getting others deactivated," he said.
The government also is seeking cooperation from Google and other Internet search engines, Singh said.
Last week federal and state ministers as well as police authorities held their breath as Assamese Muslims living and working in Bangalore engulfed the train station after rumors of the Web site information swept through their community.
Rail authorities and train companies in Bangalore, in the southwest state of Karnataka, put on extra trains to Assam in the northeast to cope with the influx of people who said they feared an outbreak of ethnic violence.
The Times of India reported that some of the Web sites had doctored images of death and destruction caused by a cyclone to appear as if the carnage was the result of an attack on Muslims in Assam.
In other videos, bodies of victims of an earthquake that occurred months ago were altered to make it appear the people had been killed by Buddhist monks, the newspaper reported.
A report by The Hindustan Times quoted Assam Chief Minister Tarun Gogoi saying he suspected "from the very beginning that foreign forces were behind this."
"It is not merely a clash between (the ethnic group) Bodos and minorities. The Union Home Ministry report that Pakistani elements were involved has vindicated our stand," Gogoi told the Press Trust of India.
"We will institute a probe to find out details regarding the involvement of foreign elements in the violence," Gogoi said.
Despite the tensions created by the Web sites, little violence was attributed to the videos.
However, some people from the northeast have been attacked in the cities of Pune in Maharashtra state and Hyderabad in Andhra Pradesh state. A Tibetan was stabbed in Mysore in Karnataka in what appeared to be a case of retaliation against alleged brutalities on Muslims, The Times of India said.
Last week Indian Prime Minister Manmohan Singh immediately called for calm as soon as the problem became known.
"All political parties must work together to give a feeling of confidence to all affected people," he told reporters at his residence in Delhi during an Iftar event -- the evening meal when Muslims break their fast during the Islamic month of Ramadan.
Thousands of people flocked to Bangalore's main train station demanding tickets back home. One day along, more than 2,000 tickets more than usual were sold to people traveling to Guwahati, the largest city in Assam.
The situation at the city railway station was chaotic as thousands of people from northeastern India and Nepal, Bhutan and Tibet nationals thronged to get tickets, The Times of India report said.
Assam, similar to other states in India's remote northeast, has an ongoing conflict between the government and several rebel groups which are demanding more autonomy or independence.