PM Manmohan Singh has appealed for calm and said peace "must be maintained at any cost".
Officials have blamed the mass exodus on "rumour mongering".
Correspondents say the rumours of attacks are linked to clashes in the north-eastern Assam state last month.
More than 300,000 people fled after fighting between indigenous Bodo tribes and Muslim settlers in Assam.
Fresh violence between the two sides was reported on Thursday when a mob burnt down a bus and a road bridge, reports say. At least nine people were reported to be injured in clashes.
The main railway station in Bangalore was flooded with migrant workers from north-eastern states for a second successive day on Thursday with over 7,000 people boarding four trains to the north-east.
Around 4,000 fled on Wednesday, a senior police officer in the city told the BBC.
There are 250,000 people from the north-east living and working in Bangalore, which is often referred to as the Silicon Valley of India.
Many of them are students, security guards and workers in the hospitality sector.
The rumours of attacks have spread to neighbouring Chennai city in Tamil Nadu state, and western Pune city in Maharashtra, reports say.
Nearly 3,000 workers and students from north-east - mostly from Assam - living in Chennai arrived at the railway station to board to special trains to take them home, one report said.
"Nothing has happened till now, but we are very sure something really bad is going to happen. Our Bangalore friends have said we have to leave," Bishnu, a migrant worker from Assam, told The Hindu newspaper.
Reports of a similar exodus are being reported from western Pune city, where 2,000 such north-east people working in the city are reported to have fled.
The rumours of attacks have been spread through text messages and the social media. There have been a few reports of people being threatened to leave.
"We must work together to ensure that all people from other states do not feel threatened by rumour mongering and text messages," PM Manmohan Singh said.
Many young people from the restive north-east region have migrated to the cities of Delhi, Mumbai and Bangalore in search of better jobs and education.
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