FDA Warning Authority: How the Agency Takes Action Against Non-Compliant Manufacturers

The U.S. Food and Drug Administration doesn’t just approve drugs and monitor food safety-it also has the power to shut down companies that break the rules. If a manufacturer doesn’t follow federal standards, the FDA doesn’t wait. It acts. And one of its most powerful tools is the FDA warning letter.

What Is an FDA Warning Letter?

An FDA warning letter isn’t a gentle reminder. It’s a formal notice that a company has violated federal laws under the Federal Food, Drug, and Cosmetic Act (FDCA). These letters are sent after inspections reveal serious problems-like contaminated products, false claims, or unsafe manufacturing practices. They’re not optional. They’re a legal trigger.

When a warning letter arrives, the company has just 15 business days to respond. That’s it. No extensions unless the FDA agrees. The letter lists every violation in detail: which section of the law was broken, what went wrong, and what needs to be fixed. If the company doesn’t respond properly-or if the fix isn’t good enough-the FDA moves to the next level.

These letters are signed by top officials now, not junior reviewers. Since early 2023, under Commissioner Robert Califf, warning letters are signed by directors of the Center for Drug Evaluation and Research (CDER) or the Center for Biologics Evaluation and Research (CBER). That change means the FDA is treating these as high-priority enforcement actions, not paperwork.

How the FDA Builds Its Case

Before a warning letter is sent, the FDA usually conducts an inspection. During that inspection, inspectors document issues using FDA Form 483. This form lists observations like dirty equipment, missing records, or unapproved ingredients. It’s not a warning letter-but it’s the first red flag.

If the company ignores the 483 or doesn’t fix the problems, the FDA issues a warning letter. This is where things get serious. The letter says: “You have violated the law. Here’s what you did. Here’s what you must do. If you don’t, we’ll take further action.”

Some violations are obvious: selling unapproved drugs, making false claims about weight loss or diabetes cures, or failing to test for contaminants. Others are more technical: not maintaining proper temperature controls during storage, not validating cleaning procedures, or not reporting adverse events. But to the FDA, all of them matter. Safety isn’t negotiable.

What Happens If You Ignore It?

Ignoring a warning letter is like ignoring a court summons. The FDA doesn’t ask twice.

If a company doesn’t respond-or if the response is weak-the FDA can escalate. The next step? Civil Monetary Penalties (CMPs). These fines can range from $10,000 to $1 million per violation. For a company selling thousands of units, that adds up fast.

Worse, the FDA can issue an Import Alert. That means any product from that manufacturer gets stopped at the U.S. border. No inspection. No chance to prove it’s safe. Just detained. The importer has 30 days to prove compliance, but most never make it past the dock.

In extreme cases, the FDA can withdraw approval of a drug. That’s the death sentence for a pharmaceutical company. No more sales. No more distribution. The product is pulled from shelves and pharmacies. The company can appeal-but the clock keeps ticking, and money keeps leaking out.

And then there’s criminal liability. If a company delays, denies, or limits an inspection-like hiding documents or refusing access to facilities-it can be charged under Section 303(f) of the FDCA. That’s a federal crime. Individuals can be fined or jailed. The FDA has been ramping up unannounced inspections, especially on foreign facilities, knowing that many violations go undetected without surprise visits.

Who Gets Targeted Most?

Not all industries get hit the same way. The FDA focuses where the risk is highest.

Tobacco products have seen over 700 warning letters since 2021. Most target companies selling unauthorized e-cigarettes and flavored vapes marketed to teens. The FDA says these products violate the premarket review requirement. Even if the product is popular, if it wasn’t approved, it’s illegal.

Pharmaceutical compounding is another hot spot. In the first half of 2025 alone, the FDA issued 58 warning letters to telehealth companies and compounding pharmacies selling fake versions of GLP-1 drugs like semaglutide and tirzepatide. These are expensive weight-loss drugs. Some companies are marketing them as “custom formulations” to avoid FDA approval. The FDA calls it misbranding. The courts are backing them up.

Food manufacturers are being held to new standards under the Food Safety Modernization Act (FSMA). In 2024, the FDA issued 149 warning letters to human food facilities for failing to implement Hazard Analysis and Risk-Based Preventive Controls (HARPC). That’s a big shift. It’s no longer enough to just clean your equipment. You have to prove you’ve analyzed every possible risk-and taken steps to prevent it.

Foreign manufacturers are under more pressure than ever. The FDA plans to increase unannounced inspections of overseas facilities by 300% in 2025-2026. Many U.S. companies rely on overseas suppliers for active ingredients or finished products. But if those suppliers cut corners, the FDA holds the U.S. company responsible. No excuses.

How Companies Should Respond

If you get a warning letter, don’t panic-but don’t delay either.

Step one: Read it carefully. Every word matters. The FDA doesn’t waste space. If they mention Section 502(a) of the FDCA, that’s about misbranding. If they cite cGMP violations, that’s about manufacturing quality. Know what you’re being accused of.

Step two: Assemble your team. Legal counsel, quality control, regulatory affairs, and senior leadership must all be involved. This isn’t a task for one person. It’s a crisis.

Step three: Fix it fast. Don’t just write a letter. Fix the root cause. If the problem is poor documentation, train your staff. If it’s contaminated batches, overhaul your cleaning process. The FDA doesn’t care about your excuses. They care about whether the problem is truly gone.

Step four: Submit a detailed response. Include timelines, photos, training records, validation reports. Show proof, not promises. The FDA will check. They’ve seen this before.

Step five: Prepare for follow-up. The FDA may send inspectors back. Be ready. If they find the same issue again, the penalties get worse.

The Bigger Picture

The FDA isn’t just cracking down. It’s changing how it operates. Warning letters used to be advisory. Now, they’re the first step in a legal process that can end in fines, seizures, or jail. The agency is centralizing decisions, increasing inspections, and targeting digital marketing-like social media posts and websites-that make false claims.

It’s clear: the days of lax oversight are over. Companies that treat FDA rules as optional are playing with fire. The agency has the tools, the funding, and the will to act. In 2026, the FDA requested $50 million more to expand inspections and enforcement. That’s not a budget line. That’s a warning.

If you’re in manufacturing-whether it’s pills, food, or vape pens-you need to know the rules. And you need to follow them. Because the FDA isn’t asking nicely anymore. It’s enforcing.