The Minister confirmed that a fundamental strategic review of NIHE is also underway.
It claims the NIHE was exposed to fraud because of major problems in the oversight of work carried out by contractors.
The Minister for Social Development Alex Attwood said the team of audit, fraud, management and personnel experts went into NIHE on Monday.
Last week NIHE chief executive Paddy McIntyre announced his retirement making it clear that his decision had nothing to do with any inquiries.
The minister said there were ongoing police investigations into NIHE as well as a number of internal probes including one by the ombudsman.
He said his department has monthly accountability meetings with the senior team in NIHE to be assured that the necessary measures are being taken.
The move is connected to two BBC investigations, one of which concerns a dispute between NIHE and one of its biggest contractors Red Sky.
In July, Social Development Minister Nelson McCausland said NIHE was failing its 90, 000 tenants - and the taxpayers who funded it - after a separate investigation into other contractors.
However, the police advised it could take no action because there was insufficient evidence of criminality and there had been "systematic errors" with the supervision of Red Sky contracts by NIHE.
Mr McCausland has pledged this autumn to unveil future plans for public housing in Northern Ireland, which could see the NIHE abolished and its dwellings hived-off to new or existing housing associations.
He gave the example of the West Winds Estate in Newtownards where grass on one side of a path was the responsibilty of the DRD and on the other the responsibility of NIHE.
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