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

The U.S. Food and Drug Administration doesn’t wait for a public health crisis to act. When manufacturers cut corners, mislabel products, or skip safety checks, the FDA responds with one of its most powerful tools: the FDA warning letter. These aren’t gentle reminders. They’re formal notices that a company is breaking the law-and if they don’t fix it fast, the consequences get serious.

What Exactly Is an FDA Warning Letter?

An FDA warning letter is the agency’s first official step in enforcing the Federal Food, Drug, and Cosmetic Act. It’s not a fine. It’s not a shutdown. But it’s the line in the sand. Issued when inspectors find violations of significant regulatory standards, these letters list specific problems-like dirty equipment, false advertising, or unapproved drug ingredients-and demand a response within 15 business days.

These letters come from the top. Since early 2023, under Commissioner Robert Califf, warning letters are now signed by directors of the Center for Drug Evaluation and Research (CDER) or the Center for Biologics Evaluation and Research (CBER)-not junior reviewers. That change signals something: the FDA is treating these violations as serious threats to public safety, not administrative oversights.

For example, in 2025, the FDA sent 58 warning letters to compounding pharmacies and telehealth companies selling unapproved versions of weight-loss drugs like semaglutide and tirzepatide. These letters didn’t just say, “Please stop.” They cited specific sections of the law-Sections 502(a) and 502(bb)-and accused companies of misbranding. The message was clear: selling fake or unapproved versions of popular medications is a direct violation of federal law.

How the FDA Builds Its Case

Before a warning letter lands on a manufacturer’s desk, there’s usually an inspection. FDA inspectors show up-sometimes unannounced-and document what they find on FDA Form 483. This form lists observations: dirty floors, missing records, failed quality tests. It’s not a violation notice yet, but it’s the first red flag.

If the issues are serious enough, the FDA follows up with a warning letter. This document doesn’t just list problems-it demands action. Companies must respond with a detailed plan: what they’ll fix, how they’ll fix it, and when. The FDA doesn’t accept vague promises. They want timelines, test results, and proof of training.

And here’s the catch: if a company ignores the letter or submits a weak response, the FDA doesn’t wait. It escalates. That could mean a recall, import detention, civil penalties of up to $1 million per violation, or even criminal charges. Under Section 303(f) of the FDCA, delaying or denying an inspection can lead to jail time.

Import Alerts and Border Enforcement

The FDA doesn’t just watch U.S. factories. It’s stationed at ports of entry. If a shipment of supplements, medical devices, or drugs arrives with violations-like unapproved ingredients or false claims-it gets detained. No waiting. No second chance.

Importers get a Notice of FDA Action explaining the violation. They have 30 days to prove the product is safe and compliant. If they can’t, the product is refused entry. This is especially common for products from overseas manufacturers that skip cGMP (Current Good Manufacturing Practices). In 2024, over 1,200 shipments were detained at U.S. borders because of FDA violations.

One major target: dietary supplements labeled as “natural” but containing hidden pharmaceuticals. The FDA has issued dozens of import alerts for these products, and they’re not going away. In 2025, more than 30% of all import alerts targeted products sold as weight-loss aids or sexual enhancement supplements.

Tobacco and Food: Two Other Fronts

The FDA’s warning power isn’t limited to drugs. In the tobacco sector, the agency has issued over 700 warning letters since 2021 targeting unauthorized e-cigarettes and flavored nicotine products. Many of these were marketed to teens with cartoon packaging and sweet flavors-exactly what the FDA’s 2025 enforcement strategy was designed to stop.

Food manufacturers aren’t safe either. In 2024, the FDA issued 149 warning letters to human food facilities and 37 to animal food producers. Most cited violations of the Food Safety Modernization Act (FSMA), specifically failure to implement Hazard Analysis and Risk-Based Preventive Controls. That means companies didn’t properly assess risks like contamination, allergens, or pathogens. One company was cited for storing raw meat next to ready-to-eat meals. Another didn’t test for Listeria in its processing environment.

These aren’t old-school hygiene issues. The FDA now expects food makers to use science-based risk models. If you’re not doing that, you’re violating the law.

What Happens If You Don’t Respond?

Ignoring a warning letter is like ignoring a court summons. The FDA doesn’t send a second letter. It moves to the next step.

First: Civil Monetary Penalties. These can range from $10,000 to $1 million per violation. For a company selling a popular drug, that could mean millions in fines.

Second: Product Recall. The FDA can force a company to pull its product from shelves. In 2025, a compounding pharmacy was ordered to recall over 12,000 vials of mislabeled semaglutide after failing to respond to its warning letter.

Third: Withdrawal of Approval. For drugs, this means the product can no longer be legally sold. For medical devices, it means the device can no longer be marketed. Once approval is withdrawn, the company must reapply-and that process can take years.

Fourth: Criminal Charges. In extreme cases, company executives can be personally prosecuted. The FDA has increased its collaboration with the Department of Justice to pursue individuals who knowingly falsify records or obstruct inspections.

Why the FDA Is Getting Tougher

The shift in enforcement isn’t random. It’s strategic. In 2023, the FDA announced it was returning to the “1990s paradigm” of issuing hundreds of warning letters per year. That’s up from just 150-200 in the early 2020s.

Why? Because the market changed. Telehealth companies started selling compounded drugs online. Overseas factories began flooding the U.S. with unapproved supplements. Social media influencers promoted unregulated weight-loss products. The old system of slow, reactive enforcement wasn’t enough.

Now, the FDA is proactive. It’s using unannounced inspections at foreign facilities-a tool it barely used before. It’s targeting digital marketing. It’s training inspectors to spot misleading claims on Instagram and TikTok. And it’s increasing its budget by $50 million in FY2026 to expand these efforts.

What Manufacturers Should Do

If you’re a manufacturer, don’t wait for a warning letter. Build compliance into your operations.

• Train staff on cGMP, FSMA, and labeling rules every year.
• Keep records clean and accessible-no redacted documents.
• Test products for contaminants and verify ingredient claims.
• Review marketing materials with legal counsel before posting.
• Designate a compliance officer who reports directly to leadership.

When a warning letter arrives, treat it like a crisis. Don’t send a generic reply. Hire an FDA lawyer. As regulatory experts at Ropes Gray LLP say, “A warning letter is a de facto regulatory emergency.”

The FDA isn’t trying to shut down honest businesses. It’s trying to stop those who put profits before safety. If you’re following the rules, you have nothing to fear. If you’re cutting corners, the warning letter is just the first step in a much longer, costlier process.