An MLA has questioned how funding was approved for businesses affected by the Primark fire in Belfast but not for firms hit by flooding.
The SDLP's Mark H Durkan has written to the head of the civil service to ask for the rationale behind emergency funding allocation.
A £1.1m recovery package has been announced for Belfast.
But in August 2017 businesses in the north west hit by flooding were told funding needed ministerial sign off.
Northern Ireland has been without a devolved government since January 2017.
MLAs from the Foyle and West Tyrone constituencies met with David Sterling, the head of the Northern Ireland Civil Service, in September 2017 to establish if the emergency financial assistance scheme could be offered to businesses affected by the flooding.
In a letter seen by BBC News NI, the Executive Office confirmed to local politicians that this scheme could not be altered to include a provision for businesses as the funding was "payable to to households and not businesses" without ministerial sign-off.
The possibility of launching a new scheme to assist business owners and farmers was also dismissed in the absence of a minister.
Hundreds of homes and businesses were flooded when record amounts of rain fell across counties Londonderry, Tyrone and Donegal on August 22.
Mr Durkan welcomed the funding for businesses in Belfast, but he said it does "little to allay the perception that citizens in our constituencies have not received equal treatment or that their plight did not warrant similar focus or consideration in their time of need".
"If the flooding had happened in Belfast, departments would have been tripping over themselves to help," he said.
He confirmed that he has asked Mr Sterling to "provide the rationale" for when tailored assistance can be provided in some cases without ministerial sign-off but not in other cases.
A spokeswoman for the Executive Office said Mr Sterling had received the SDLP MLA's letter and would "provide a response in due course".