This treatment helps relieve symptoms of the menopause and it is estimated that the shortage is affecting one million women in Britain.
Symptoms for those who cannot get the correct HRT medication can include migraines, hot flushes and back pain.
Several pharmacists in the district spoke to the Middy about the recent difficulty of sourcing HRT medication.
Raj Patel, pharmacist at Orchards Pharmacy in Haywards Heath, said: "It's mainly the patches we've been having a hard time getting, and the gel."
He said that if a customer comes in with a prescription for a brand they do not have, they can ask their surgery to redo the prescription for one they have in stock.
But this could take an extra couple of days.
Mr Patel said: "Sometimes if they need it more obviously they'll take their prescription to see if another pharmacy has it."
He recommended customers call in advance to see what pharmacy has in stock before getting a prescription.
Pharmacist Richard Hopkins, owner of Hopkins Pharmacy in Burgess Hill, said shortages are a normal issue but that sourcing HRT medication has been a problem recently.
"The demand for HRT has gone up," he said, adding that his issue has been with Oestrogel and patches.
Mr Hopkins said he is now rationing HRT medication and encouraged people to phone their regular pharmacy to see what is available.
He said shortages normally happen because medicines are manufactured all over the world.
"All it takes is a factory to lose it's license, or move, or have a problem with the raw materials," he said.
Pharmacist Victor Andrews from Ditchling Pharmacy called the HRT shortage 'a huge national problem'.
But he said: "We do try to give out a month's worth just to keep patients ticking over."
He also said the Government had issued serious shortage protocols (SSPs), allowing pharmacies to give out lower quantities than the prescription states.
On April 29 the Department of Health and Social Care said SSPs were issued to limit dispensing to three months’ supply of Oestrogel, Ovestin cream and Premique Low Dose tablets to make sure women can access HRT products reliably.
"We try and distribute it as evenly and fairly as possible," said Mr Andrews.