The NWC, which owns the Northern stores, lost its NNI status on April 1.
The company is the largest private-sector employer in Nunavut with more than 800 workers, 74 per cent of whom are Inuit.
The NWC has been active in Nunavut for more than a century.
The NNI policy gives Inuit-owned businesses an advantage when bidding on government contracts.
Companies must be 51 per cent Inuit owned to meet NNI policy criteria.
Len Flett, vice-president, store development and public affairs, says the NWC has sent a new proposal to the Nunavut government and Nunavut Tunngavik Inc. (NTI) to regain its NNI status.
The submission includes a proposal to establish a best practice management-training centre in Baker Lake.
"Our Baker outlet is the most efficient store operation we have and we want other stores to emulate the practices its manager (Allan Hart) has in place," says Flett.
"Plus, Baker is fairly centrally located in relation to our other stores in Nunavut."
The NWC's plan is to rotate store and department managers, and supervisory staff through the Baker store.
Flett says supervisors will spend three to four weeks in Baker, depending on the training they receive.
Most of the training will be department-specific, such as meats, produce and Quick Stop management.
General training would also be conducted in overall store management and areas such as foods and general merchandise.
"The department-specific training has already started and we plan to start rotating some of our managers for overall store management training in July.
"We have 30 people scheduled to go through the Baker Lake store for training this year."
Flett says the NWC doesn't have a dedicated timeline to initiate its proposal, other than to get underway as quickly as possible.
He says delays with disagreements over the NNI policy between the GN and NTI are hampering NWC's decisions.
"We don't have a clear idea on where we want to go in regards to further investments in Nunavut.
"I will be travelling to Iqaluit this month to meet with NTI and the GN, so the lines of communication appear to be open."