Meat Hygiene Service auditors are to visit 37 licensed cold stores in NI as part of an investigation into a meat cold store in County Fermanagh.
Move was prompted by inquiry at County Fermanagh cold store
The Food Standards Agency said it would begin the visits immediately and focus on whether products bearing illicit health marks were present.
The agency is continuing to investigate a meat cold store operated by Euro Freeze Ireland (Ltd) in Lisnaskea.
The agency is investigating alleged repackaging and relabelling of meat.
The authorities seized a substantial quantity of meat at the premises in November.
The agency has linked the search of the cold store at Lisnaskea to the seizure of poultry meat - believed to have originated from China - at Belfast docks.
While no human health issues have emerged from the Euro Freeze investigation, inquiries by food safety organisations on both sides of the Irish border are continuing.
Dr Jon Bell, chief executive of the FSA, said the investigation had "highlighted some possible issues around operation and supervision of cold stores in Northern Ireland".
"It is important that we do not wait until the investigation is complete before establishing whether the system is largely working well or whether there are more widespread grounds for concern.
"This investigation may offer reassurance, or it may identify areas for remedial action. Either way, it is important that there is external scrutiny of the system and we identify any specific issues where action may need to be taken."
Earlier this month, it was announced that meat hygiene inspectors were being brought in from Britain to scrutinise the work of Department of Agriculture veterinary staff at Northern Ireland cold stores.