In a statement on Friday it emerged that Icelandic bank Kaupthing was 'uncertain' over the£200 million deal after Nisa-Today's shopkeepers last month accused the two companies of 'acting as a cartel'.
A spokeswoman for Nisa-Today's - which has a membership of 700 independent wholesalers and retailers, each with an equal share in the business - said there would be a board meeting today to decide what to do.
Asked if the move by the bank meant that the merger was off, she replied: 'It certainly looks that way.'
The merger between Nisa-Today's and Costcutter was first proposed in May and has been dogged by controversy ever since.
The boards of the two companies argued that the tie-up was necessary in order to 'survive' as Tesco and other large retailers moved into the convenience store market.
In order to placate Nisa-Today's members, the two boards had to increase their proposed shareholding in the business from 40 per cent to 60 per cent.
There were also protests over the£9 million golden goodbye set to be paid to Nisa-Today's founder and chairman Dudley Ramsden as part of the deal.
The latest hitch came after an independent committee of non-executive directors appointed by Nisa-Today's found the accusations that the two companies were acting like a cartel were untrue.
Despite this, Kaupthing demanded that further conditions were attached to the proposed payment structure of the deal in order for it to proceed.
Nisa-Today's said on Friday that it 'cannot recommend the revised proposals' as they were not in its shareholders' 'best interests'.