Some Boots pharmacy staff claim they are under too much pressure and that mistakes could be made as a result.
A number of current Boots pharmacists told BBC Inside Out that understaffing could pose a risk to patients.
One whistleblower, a former manager, said he resigned in 2015 after he took his concerns to the independent industry regulator.
Boots, however, refuted the claims. It said its pharmacies were not understaffed and pointed out its industry-leading patient safety record.
Former employee Greg Lawton, who worked for Boots between 2008 and 2015, told the BBC that the things he knew about staffing levels kept him awake at night.
In 2012 he worked on an investigation ordered by Boots into stores with the highest levels of dispensing errors.
He said: “We spoke to pharmacists, to store managers and to area managers and what those people were saying [was that] absolutely staffing levels was flagged as an issue, poor staffing levels.”
Boots said that after the investigation it implemented a detailed action plan.
It commissioned academic research which, it says, found that pharmacies with higher levels of dispensing staff were associated with higher error rates.
Boots said it found no record of staff raising concerns with the area manager.