Costcutter is partly financing the deal through an agreement with Icelandic bank Kaupthing.
An unofficial meeting of a significant number of retailers is planned for next Monday.
One source said many retail members were "outraged" at the plans, because they would compromise the company's ethos as a mutual business.
They also claimed that some board members were set to gain significantly more than retail or wholesale members.
Nisa-Today's has about 700 retail and wholesale members that hold roughly equal shares in the company and stand to gain up to £50,000 through the deal over three years. Shareholders are scheduled to vote on the proposals on July 3.
It is understood that Colin Graves, executive chairman of Costcutter, and Nisa-Today's chairman Dudley Ramsden will each get a 10% stake in any new entity. It is rumoured that Ramsden will receive an additional payment for brokering the deal.
Five Nisa-Today's board members are understood to be planning to buy a combined stake in the business.
Wholesale members have protested that they were only informed of the board meeting that aired the merger plan on the day it took place (Wednesday, May 10). "I think there will be a lot of resentment about this," said one.