India says rumours and text messages that triggered an exodus of migrant workers from southern cities originated in Pakistan.
Some 30,000 people have fled the cities of Bangalore and Mumbai since Wednesday. Extra trains have been provided to allow them to return home.
They come from indigenous communities in the north-eastern state of Assam, where there has been fighting with Muslim communities.
The messages threatened revenge attacks against them by Muslims.
Indian Interior Minister RK Singh said the bulk of the messages had their origin on various websites in Pakistan.
He said India would protest to Pakistan, but gave no further details about who may have sent the messages or posted the images.
The BBC reports there has been no official reaction from Pakistan.
On Friday, the government imposed a ban on bulk text messages to try to stop the panic.
At least 78 people have died and more than 300,000 have been displaced in clashes in Assam, mainly between the Bodo tribe and Muslims.