Retailers' return on the title was slashed from 9.68p to 8.47p from March 8, a 12.5% reduction.
The move follows cover price reductions on The Sun and The Daily Star in recent months, which also squeezed shops' profits, and re-opens the debate on how newsagents should restore their income.
Stefan Wojciechowski, head of news and magazines at the National Federation of Retail Newsagents, called the cut "despicable" and warned of a backlash from Scottish retailers who were "the pawns in a price-war chess game conducted by publishers".
He continued: "No doubt many Scottish newsagents will now be considering whether they can make more profit by using the space to sell something that provides a better return. Others, aware that they have the right to set their own selling price on newspapers, will be giving further thought to this option."
Wojciechowski stressed that only individual newsagents could decide whether they would continue to support the Express.