The Direct to Retail service, which starts from July, will see some 6,000 stores receive NI titles direct from company.
A daily charge of £1.75 will apply to all stores, irrespective of their size or volume of sales, on top of other wholesalers' carriage service charges (CSCs) for other publishers' titles.
NI said the charge was "the net cost of delivery and collection - not an area for profit."
Chief operating officer Clive Milner said NI would expect the wholesalers to reduce their CSCs to affected stores in proportion to the weight on NI titles no longer delivered by their vehicles - about one-third of all newspapers. He said the publisher had made this point to the Office of Fair Trading, but could not influence wholesalers' contracts with retailers.
Retailers expressed doubt that Smiths News and Menzies Distribution would voluntarily lower carriage charges. Neither was prepared to comment as C-Store went to press.
NI head of wholesale and retail operations Nigel Lomas said the system would improve accuracy and timeliness of deliveries. "By taking control of distribution we will be able to help retailers grow sales," he added.
"These changes are necessary to help safeguard our future. Retailers are the vital link between us and our readers and we are making this investment now to build long-term, successful relationships."
Advertising revenues in NI's UK newspapers fell by 21% year on year in the three months to March.