Managing Medicine Shortages in Your Pharmacy

Medicine shortages used to be an occasional emergency. They are now a permanent operating condition. On any given day there are about 400 medicines in short supply in Australia, roughly 30 of them critical. A critical shortage means a serious risk to patients with no ready substitute. This is not a passing disruption you can wait out. It is the new normal, and the pharmacies that cope well are the ones with a system rather than luck.

This guide sets out that system: how to see shortages coming, substitute safely, communicate clearly, and stop losing hours every week to chasing supply.

Why shortages are now normal

The causes are structural. Most active ingredients are made at a small number of plants worldwide, so a single manufacturing fault or raw-material delay can empty shelves across whole countries at once. In Australia the same six categories keep coming up short: antibiotics, anaesthesia and pain relief, heart and blood pressure medicines, hormonal treatments, cancer therapies, and epilepsy medicines. A nationwide shortage of sterile fluids has run since 2024.

It is not only an Australian story, which is worth remembering if you serve a community that reads widely about their medicines. Across Europe the picture is as bad or worse: in the most recent survey, 96 percent of countries reported shortages persisting at high levels, with more than 600 medicines in shortage across a third of them. In the Netherlands alone there were 2,292 registered shortages in a single year, affecting around 5 million people.

The real cost to your pharmacy

Shortages are expensive in the currency you have least of: time. The average European community pharmacy now spends about 12 hours a week just managing shortages, a figure that has climbed steadily year on year. That is time your pharmacists spend on the phone to wholesalers and prescribers instead of with patients.

The other cost is trust. When a patient cannot get their usual medicine, the pharmacy is the face of the problem even though it did not cause it. Reduced patient trust is now the single most frequently cited consequence of shortages, and 89 percent of countries report shortages actually interrupting treatment. A calm, well-handled substitution is one of the strongest trust-builders you have.

A system for managing shortages

You cannot fix the global supply chain. You can build a repeatable response so that a shortage is a managed event rather than a scramble.

See it coming

The worst version of a shortage is the one you discover when a patient is standing at the counter. Watch the shortages that matter to your patient mix rather than the whole list. The TGA maintains a public database of current and anticipated shortages, and your own low-stock alerts are the earliest warning of all. A fast-mover trending down toward its reorder point is your cue to act while you still have options.

What to do when a medicine is out of stock

When a line goes short, speed comes from preparation. Keep a ready reference of the common alternatives for your high-volume medicines: the equivalent brand, the different strength you can combine, the therapeutic alternative, and the rule that lets you supply each one.

The rule is the part that trips people up. When the TGA has issued a Serious Scarcity Substitution Instrument (SSSI) for a medicine in short supply, a community pharmacist can supply the specified substitute without prior approval or a new prescription, and simply notifies the prescriber afterwards. Where no SSSI is in force, agree the substitution with the prescriber first. For some shortages the alternative is a Section 19A overseas-registered product the TGA has approved for temporary supply.

Option	When to use it	What authorises it
Same medicine, different brand	A generic or alternate brand is in stock	Usual brand-substitution rules
Different strength or form	The prescribed dose can be made another way	Prescriber, unless an SSSI covers it
Specified substitute under an SSSI	The TGA has issued an SSSI for the shortage	The SSSI itself, no prior prescriber approval, notify after
Section 19A product	An approved overseas-registered equivalent exists	TGA Section 19A approval
Therapeutic alternative	No direct substitute is available	Prescriber

Knowing which path applies turns a twenty-minute problem into a two-minute one.

Communicate clearly

Tell the patient plainly what is going on, what you are doing about it, and when to check back. Contact the prescriber early with a proposed alternative rather than a bare problem, so the conversation is a decision, not a diagnosis. Patients forgive a shortage they did not cause. They remember being left in the dark.

Track and learn

Record which lines went short and how you resolved them. Over a few months this becomes a map of your real supply risk, and it tells you which critical fast-movers deserve a slightly deeper buffer so the next gap does not reach the patient.

Where Krepko fits

Seeing a shortage coming is a stock-data problem, and it is one the team behind Emily, our AI voice agent, is building for. Krepko is developing an inventory system for pharmacies that surfaces low-stock and near-expiry alerts on the dashboard, with supplier and batch data linked to each product. An at-risk line flags early enough to substitute before the shelf is empty, not after.

It is in development rather than available today, but if managing shortages is eating your week, it is being built to give you that head start. You can join the waitlist to hear when it lands. Shortages and medicine recalls are the two supply-disruption events every pharmacy has to handle well. For the ordering side, see our guide to setting stock par levels and reorder points, and for the flip side, reducing pharmacy inventory holding costs.