The announcement follows an investigation by the Times newspaper into properties run by Jomast, a subcontractor for security giant G4S, which provides asylum accommodation in the northeastern town of Middlesborough.
Local asylum seekers told the Times they had been verbally abused, had their properties vandalised and had the sign of the far-right National Front carved on their front doors.
"I am deeply concerned by this issue and I have commissioned Home Office officials to conduct an urgent audit of asylum seeker housing in the north-east," said immigration minister James Brokenshire.
The Times identified 168 properties run by Jomast, 155 of which had red front doors. The newspaper contacted the residents of 66 properties, 62 of whom were asylum seekers.
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"When people see them (the red doors), everyone knows it means asylum seekers," said one man whose house was vandalised.
G4S said there was "categorically no... Policy to house asylum seekers behind red doors" and that it had ordered Jomast to repaint some of the doors.
Local resident Suzanne Fletcher said the issue had been raised for four years.
"The police obviously have done everything that they can do but because asylum seekers are so vulnerable, they are frightened of jeopardising their case, things haven't always been reported," she added.
Local police declined to comment.