Correspondents say the rumours of attacks may be linked to recent clashes in the north-eastern state of Assam.
More than 300,000 people fled after fighting between indigenous Bodo tribes and Muslim settlers in Assam.
There has been tension between indigenous groups and Muslim Bengali migrants in Assam for many years.
The main railway station in Bangalore was flooded with migrant workers from north-eastern states after rumours spread on Wednesday.
The railways ran special trains to the north-east to cope with the rush, officials said.
There are 250,000 people from north east living and working in Bangalore, many of them students.
Around 4,000 fled on Wednesday, a senior police officer in the city told the BBC.
He said that rumours about possible violence were spread by text messages.
"We will soon catch hold of people who sent out these messages," said the police officer.
Chief minister Jagdish Shettar told the Press Trust of India that he had told Prime Minister Manmohan Singh: "There is no untoward incident nor is there any threat to people of north-eastern states [living in Bangalore]."
He added: "I promised that necessary steps would be taken to give protection to these people."
The rumours came a day after a 22-year-old Tibetan student was allegedly attacked in Mysore city near Bangalore by two people who suspected him of being from the north-east.
Insurgency and violence have marked life in the north-eastern region for many years.
Many young people find it safer to leave their homes and head to the cities of Delhi, Mumbai and Bangalore in search of better jobs and education.
A large number do manage to find a better life, but this sometimes comes at the cost of racial abuse.
Several cases of racial violence against north-eastern youths have been reported in Delhi, Mumbai and Bangalore in the recent past.
It is believed that most were targeted due to their distinctive appearance and different culture.
The Indian Home Ministry recently asked state governments to take stern action against those who racially abuse students from the north eastern states.
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