"Livid" and "baffled" customers have been complaining to Boots after receiving their prescriptions in plastic bags rather than paper ones.
One was so incensed she took her bag back to the store with "shame on you!" and "paper, not plastic!" written in capitals in black marker pen.
Boots said it was using plastic bags because some prescriptions are now assembled at a central location, rather than in local pharmacies.
Plastic was "more durable", Boots said.
"When items are bulkier or have to travel longer distances, we use a plastic bag as these are more durable and help us to protect patient confidentiality and support patient safety," the Nottingham-based company said in a statement.
"Central dispensing accounts for less than 8% of our total dispensing; the overwhelming majority of our prescriptions are still dispensed in paper bags."
Boots UK signed up to the UK Plastics Pact last year and said at the time it was "committed to reducing single-use plastic".
Roisin Moriarty said she was initially puzzled when she was given a plastic bag but became "increasingly angry about it as I went back to work".
"I told my colleagues, who were equally appalled, then decided I could not let it lie," she said.
"I scrawled 'SHAME ON YOU!' and 'PAPER, NOT PLASTIC!' on it in black marker pen and took it up to the pharmacy counter with an overly-polite, 'This is for whoever cares to take any notice' then walked out."
She said she intended to use a different pharmacy if Boots gave her another plastic bag.
Why is Boots using plastic prescription bags?
The majority of prescriptions are still dispensed in Boots stores in paper bags.
However, some repeat prescriptions are assembled at a "Dispensing Support Pharmacy" (DSP) in Preston and these prescriptions are sealed in plastic bags.
The bags are filled automatically by machine, so Boots said they needed to be "robust".
"The bags also need to be heat-sealed shut, which reduces the risk of products falling out of the bags in transit," the company said.
Boots pharmacy staff have previously told the BBC they were under too much pressure and feared mistakes would be made, while some patients have died due to dispensing errors.
Boots said the DSP helped to "remove some of the routine dispensing workload from individual stores so that we can free up our pharmacists to better support patient care in store".
Another customer, Jack, said he was "baffled" when he collected his prescription in a plastic bag.
"For five years I've collected my prescriptions in paper bags," he said.
"Essentially it looks like a cost-cutting exercise for the company by making things centrally.
"They either need to go back to the old model or find a way of doing it the new way without plastic."
A Boots staff member said stores have had to come up with their own "solution" to deal with customers complaining.
"I work in Boots stores that respond to these complaints by putting a note on such patients' files to repackage their prescriptions into paper bags once they are received in plastic from DSP," he said.
"This hides the use of plastic from customers and results in increased wastage as now both a plastic and a paper bag are being used for their prescriptions.
"I can only imagine how upset customers would be if they knew this was the action taken as a result of their complaints."
However, Boots said this process is "incorrect".
It said in a statement: "If a customer does not want to receive a prescription in a plastic bag, they should ask at the pharmacy.
"The pharmacy should then make up that prescription in the store directly and put it into a paper dispensing bag, rather than send it to our DSP for processing."
The staff member said: "To the best of my knowledge Boots head office have never issued any communication addressing how to deal with patients being upset at the use of plastic.
"My view is that they don't want to highlight the option for patients to opt out of DSP dispensing due to workload management and resourcing reasons."
Customer Bob Knightley complained to Boots after he received his prescription in a plastic bag in April.
"They deserve to lose more customers for such a bad decision," he said.
"They charge you for a plastic carrier bag to discourage using plastic, then introduce a system that replaces paper bags with plastic ones."
Liz Jones, who complained to Boots about her husband's medication being in a plastic bag, said: "They used to be all put in a paper bag and stapled at the top perfectly safe, strong and as environmentally friendly as possible."