According to reports the homes in Teesside are owned by Jomast, a subcontractor of services giant G4S, and were painted red so employees knew which were occupied by asylum seekers.
Would-be refugees from Syria and eastern Europe told an investigation by The Times they had been targeted as a result. One woman claimed yobs shouted: "F*** you dirty women. Get out of our country."
Another said a National Front logo was carved in their red front door.
G4S and Jomast have strenuously denied the claim that the colour was used deliberately, but recognised that "the majority" of doors in the housing stock were red.
Immigration minister James Brokenshire said in a statement: "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.
"I expect the highest standards from our contractors. If we find any evidence of discrimination against asylum seekers it will be dealt with immediately as any such behaviour will not be tolerated."
According to The Times investigation, of the 168 Jomast houses it identified in two of Middlesbrough's most deprived areas, 155 had red front doors.
The newspaper spoke to people living at 66 of the red-door houses. It said 62 were home to asylum seekers of 22 nationalities.
Of the four remaining properties two housed "former asylum seekers" and two housed British citizens.
G4S holds the Home Office contract for housing asylum claimants in the North East.
The contractor stressed its asylum accommodation is inspected frequently by the Home Office and has been found to "meet the required standards".
It said in a statement: "Our subcontractor Jomast has no policy to house asylum seekers behind red doors, although they do accept that the majority of doors, for both private and asylum accommodation, are painted red.
"Although we have received no complaints or requests on this issue from asylum seekers we house, in light of the concerns raised Jomast has agreed to address the issue by repainting front doors in the area so that there is no predominant colour.