Knives used for cutting raw meat were also used to open bags of cooked meat, admitted James Murray, assistant manager of the shop in Wishaw, Lanarkshire.
Up to 21 elderly people died from November 1996 onwards in Lanarkshire and central Scotland from the outbreak.
Mr Murray's disclosure came on the 13th day of the fatal accident inquiry into the deaths, held in Motherwell, when he was being questioned about practices in the shop.
Knives were cleaned at the sink - but he agreed in cross-examination that "sometimes" staff would then wipe them dry with a finger.
Mr Murray also said that staff would not invariably wash their hands between serving raw and cooked meat. "They kept themselves very clean. Whether they did it every time, I could not say that," he said.
But he denied a suggestion from Angus Stewart QC, for health authorities, that the shop had become "an infection superstore".
Mr Murray was questioned over the staff's motives for arriving early at the shop on 23 November 1996, ahead of a visit by environmental health officials.
Mr Murray said that John Barr had arranged for managers to go in to put cooked meat aside for the health officials.
The inquiry continues today.