What Inspectors Are Finding When Contamination Control Falls Short

Regulators are taking a much closer look at how companies are managing contamination risks.

Most sites do have a Contamination Control Strategy (CCS) in place now, which is a good thing. But that doesn’t mean they’re in the clear. Inspectors are still raising concerns when strategies are missing key details, haven’t been updated in years, or don’t match up with what’s actually happening on the shop floor.

The message is clear: a CCS that looks good on paper isn’t enough. It needs to be real, current, and backed by data.

Supporting Contamination Control with Data.

When the CCS Is Out of Date or Too Vague

One of the most common things inspectors are flagging is a CCS that hasn’t been reviewed in a long time. In some cases, companies have changed their facility layout or brought in new equipment, but no one thought to update the strategy. In Europe, this is now a direct breach of Annex 1.

Another issue is vagueness.

Some strategies state that people are the highest contamination risk, which is true, but they stop there. They don’t explain what’s being done to reduce that risk or how operator performance is being tracked. Inspectors are looking for details. What training is in place? Are operators being observed? Is there data to show the controls are working?

A strong CCS doesn’t just name the risks. It explains how those risks are being managed and how the controls are checked over time.

Environmental Monitoring That Doesn't Link Back

Environmental monitoring is supposed to be one of the ways companies confirm their CCS is working. But often, monitoring programs are running on autopilot. The data is being collected, but no one’s really using it.

In one case, the FDA found that a manufacturer wasn’t doing any air monitoring during aseptic filling in ISO 5 areas. Surface samples were only taken once a week, even though production was happening every day. On top of that, when microorganisms were found, they weren’t being identified. This made it impossible to spot patterns or recurring issues.

Even when sites have decent monitoring in place, inspectors often find that the data isn’t connected back to the CCS. That makes it hard to show whether the strategy is working.

If you can’t use your monitoring results to confirm your process is under control, inspectors will question the whole system.

Cleaning and Disinfection That Don't Hold Up

Cleaning is another area where regulators continue to find problems.

The most common issue? Procedures that haven’t been validated.

In a handful of inspections, it turned out that the sites had never validated its cleaning process for critical equipment. There were no defined hold times, no recovery studies, and no proof that the cleaning method actually removed microbial or chemical residues. That means there was no assurance that the equipment was truly clean before the next batch.

Disinfectants are another concern. Some sites are still using disinfectants without confirming they work against the actual environmental isolates found in their cleanrooms. It’s no longer enough to rely on general claims. Inspectors want to see that cleaning agents are effective in real conditions, not just in lab tests.

The expectation is now very clear.

Cleaning procedures need to be validated. Disinfectants must be shown to work against the organisms present in your facility. And all of it should be reviewed and updated regularly.

Bringing the CCS to Life

Having a CCS on file is just the beginning.

What really matters is whether it reflects your current process, how well it’s implemented, and if it’s supported by actual evidence. A good CCS ties together all the key controls, from environmental monitoring to cleaning validation, and shows how each one contributes to reducing contamination risk.

When a CCS is vague, outdated, or disconnected from daily operations, it becomes just another document on a shelf. Inspectors are paying close attention to this. They want to see a living strategy that evolves with the process and is reviewed regularly.

If your CCS isn’t doing that, it might be time to take another look.

Don't Let Your CCS Become Just Another Binder on the Shelf

At Pharmalliance Consulting Ltd, we help manufacturers turn their Contamination Control Strategy into a practical, data-driven framework that inspectors trust, and teams actually use.

From linking EM data to real risks, to validating cleaning procedures and aligning your CCS with daily operations, we support sites in making contamination control a living, evolving part of the process.

Explore our CPD-certified Contamination Control Excellence Program: https://www.pharmalliance.ie/ccs-excellence.

Because a compliant CCS isn’t just written. It’s proven.