India has blamed Pakistan for posting threatening messages on the Internet that triggered a mass exodus from Bangalore and Mumbai by migrants fleeing to their homes in the northeast.
"Our agencies have discovered that bulk of these messages have been uploaded on various websites in Pakistan," Home Secretary R.K. Singh told reporters on Saturday.
"This is a first of its kind and we believe that it is highly reprehensible."
The exodus was sparked by threats sent via mobile phones and the Internet that people from northeastern Assam state would be attacked by Muslims after the end of the holy month of Ramadan in reprisal for recent ethnic violence.
Local media reports estimated that over 35,000 people have fled the cities of Bangalore and Mumbai in recent days.
Extra trains were arranged to accommodate panicked students and workers.
Three weeks of clashes in remote Assam between members of the Bodo tribal community and Muslims have claimed at least 80 lives and displaced more than 400,000 people.
Singh said India would register a formal protest with Pakistan.
"We will raise this issue with Pakistan... I am certain that they will deny out of hand but our technical people are definite," he said.
India has banned bulk text messages temporarily to try to halt the spread of threats and incendiary rumours. Police in southern city of Bangalore have also arrested three people for spreading images and video clips across India.
The images of atrocities allegedly on Muslims sparked tension and people hailing from the northeast were attacked in western and southern cities.
Prime Minister Manmohan Singh said those who were fanning the rumours should be punished, saying "communal harmony" was at stake.
India and Pakistan have fought three wars since independence in 1947, two of them over the Himalayan region of Kashmir, which is divided by a heavily militarised Line of Control and which both countries claim in full.
Last year they resumed their tentative peace process, which collapsed after Islamist gunmen from Pakistan killed 166 people in Mumbai in November 2008.