Pharmacists are paid for each prescription they dispense.
Patients with a thyroid disorder should be exempt from the widespread trend of giving just 28 days' worth of medication at a time, campaigners say.
As well as being inconvenient, they say it means the NHS in England is paying for unnecessary prescriptions.
Around 18m scripts for underactive thyroid medication were issued in 2007, but campaigners say the number would be cut if they were issued for longer.
The NHS says it offers 28-day scripts to cut down medicines wastage.
The thyroid gland produces hormones that keep the metabolism functioning effectively.
Having an under-active thyroid means not enough of the thyroxine hormone is produced, causing a range of symptoms including tiredness, weight gain, lethargy and potentially heart failure and angina.
Patients are treated with synthetic thyroxine, which they need to take for life.
A study carried out by Newcastle University has found prescriptions for thyroid medication in England more than doubled over the last decade.
The 28-day prescription rule has been introduced by primary care trusts in a bid to cut the costly trend of medicines being wasted because people failed to finish a course.
The cost of a 28-day thyroxine prescription is £1.12 - but pharmacists are also paid a 90p fee for each script they dispense.
The Newcastle University team, led by Dr Simon Pearce, say the cost of treating a patient with thyroxine for a year with 28-day prescriptions is £26.20, whereas issuing scripts every 84 days costs £18.40.
GPs do have discretion to write longer-lasting prescriptions for people with long-term conditions, but campaigners say many are not doing so.
A survey of 2,500 people for the British Thyroid Foundation (BTF) found 38% had been given 28-day prescriptions and 17% had gone without thyroxine because of difficulties getting hold of the medication.
Janice Hickey, director of the BTF, said: "The situation is inconvenient for patients, especially if they are elderly or live in a rural area, and it also reminds people they've got a health problem.
People with Addison's disease, a rare disorder brought about by the failure of the adrenal glands are also affected by the 28-day rule.
They need lifelong treatment with steroid replacement therapy is required, and patients can become ill very quickly if do not have access to medication.
Professor John Wass, chairman of the Society for Endocrinologists - the specialists who treat patients with thyroid disorders and Addison's, said: "This is happening because PCTs are trying to save money on the cost of wasted drugs.
"But people with chronic conditions, whose lives depend on it, aren't going to waste their medication, and this means they are having to go to their doctor 12 times a year and get 12 prescriptions.
"It's completely ludicrous."
Elizabeth Wade, from the PCT Network at the NHS Confederation, said: "There's a very good rationale behind 28-day prescribing.
"We know the NHS wastes millions and millions of pounds on prescribing medicines that don't get used properly.
"Even with long-term conditions, it's right that people get their medicines reviewed on a regular basis.
"But a policy like this can be reviewed at the discretion of the individual prescriber, if patients feel they have exceptional circumstances."
A Department of Health spokeswoman said there had been no government directive to specify the length of time for which prescriptions should be issued.