Stella Buller was recovering from the birth of her first child when the NHS letter arrived. It warned her that she could face fines and charges of up to £435 for claiming four free prescriptions during her pregnancy.

Buller, 29, like all pregnant women in England, should have been exempt from prescription charges until 12 months after she gave birth. But she was never issued with a maternity exemption certificate and has now been told that the oversight makes her ineligible for free medication. She has been given three months to pay the cost of the prescriptions she collected during her pregnancy, or face three-figure penalty surcharges.

“Getting a letter that implied I’d committed an offence was horrible,” she said. “The prescriptions were all related to my pregnancy and since I’m on basic maternity pay, the sums demanded will cause me real hardship.”

Buller is just one of thousands of expectant mothers who have been similarly penalised for falling foul of NHS red tape, the Observer has learned.

Last year, the NHS Business Services Authority, the public body that checks patients’ right to exemptions on behalf of the health service, issued 38,191 letters questioning the eligibility of women who claimed a maternity exemption. More than 80% of those subsequently received a penalty charge notice because they could not produce a valid certificate.

Under NHS rules, pregnancy does not qualify women in England for free prescriptions unless their midwife registers them for a maternity exemption certificate that pharmacists are legally required to request.

But two things frequently appear to go wrong: midwives make errors on applying for the certificates, or forget to apply at all, and pharmacists fail to ask for proof of exemption.

This means that women whose certificates don’t materialise may claim free prescriptions for months without realising they are ineligible. They then face backdated bills for their medication, plus fines amounting to five times each prescription charge up to £100.

“‘For any patient group to routinely get fines on such a scale for accessing a service is extraordinary,” said Stella Creasy, a Labour MP. “I’ve had women in my constituency who have been given the wrong forms or not issued with a form at all and now find they have a fine of £100 through no fault of their own.”

Alexa Andrews received a demand to pay for antibiotics prescribed following a C-section and now fears she’ll be billed for more than 50 prescriptions claimed during her pregnancy. This could add up to more than £500. Like Buller, the 29-year-old was diagnosed with gestational diabetes and ticked the maternity exemption box on her prescription forms, unaware that she needed a certificate. A year later, she discovered she had never been registered for one.

“I’ve been sent a letter telling me I face charges and a fine of up to £100 for medication I collected in September,” she said. “The pharmacy never mentioned a certificate. I’m already struggling with post-natal depression and a reduced income and am living in fear that I may at any moment in the future get a £100 fine for each of my prescriptions over the last 12 months.”

Laura Hegarty was ordered to pay backdated bills for medication issued during her complex pregnancy, despite a written admission from her midwife that she had forgotten to register her for an exemption certificate. “Reportedly because of legislation, common sense can’t prevail over a clerical error and all my prescriptions still needed to be paid for, even though they accept I was pregnant at the time,” she said.

The Business Services Authority’s brief is to crack down on prescription fraud, but it has been accused of penalising patients who acted in good faith. In 2019, a parliamentary select committee concluded that the penalty charge process is a “heavy-handed rush to judgment” on the part of the authority and it accused the Department of Health and Social Care and the NHS of “being shockingly complacent” about patients being unfairly penalised.

The Business Services Authority claims it is hamstrung by government regulations that state that exemptions can’t be backdated by more than a month, even if a patient can prove her pregnancy dates.

The health department told the Observer it had no plans to allow exemption certificates to be backdated by more than a month, even when NHS error was to blame. It said: “NHS Business Services Authority promotes maternity exemption certificates through a variety of channels and there is clear guidance for patients and healthcare practitioners to register for them.”

The General Pharmaceutical Council, which regulates pharmacists, declined to comment.

Creasy said: “The law has to change so that where women are entitled and it’s clear they are, they don’t face fines because the NHS didn’t get its act together to issue them with its own exemption.”

• This article was amended on 6 February 2023. The General Pharmaceutical Council regulates pharmacists, it does not represent them as an earlier version said due to an editing error.