FDA Warning Authority: How the Agency Enforces Compliance Against Non-Compliant Manufacturers

The U.S. Food and Drug Administration doesn’t just approve drugs and foods - it actively shuts down companies that break the rules. Since the 1970s, FDA warning letters have been the agency’s go-to tool to call out manufacturers who violate safety, labeling, or manufacturing standards. These aren’t gentle reminders. They’re formal notices that say: fix this now, or face serious consequences.

What a Warning Letter Really Means

A warning letter from the FDA isn’t a suggestion. It’s a legal signal. When the agency finds violations during an inspection - like unsafe ingredients, false claims on labels, or dirty production facilities - it sends a letter listing each problem. These letters are issued under the Federal Food, Drug, and Cosmetic Act (FDCA), the law that gives the FDA its power.

The letter tells the company exactly what they did wrong, cites the specific law or regulation broken, and gives them 15 business days to respond with a plan to fix it. If they don’t respond, or if their plan is weak, the FDA doesn’t wait. They move to the next step: fines, product seizures, import bans, or even criminal charges.

Recent changes have made these letters sharper. In 2023, FDA Commissioner Robert Califf announced a return to the 1990s style of enforcement - meaning hundreds of warning letters per year, not dozens. Today, these letters are signed by top officials like the Director of CDER or CBER, not mid-level reviewers. That change sends a message: this isn’t just paperwork. It’s a top-priority enforcement action.

How the FDA Picks Its Targets

The FDA doesn’t go after everyone equally. Some industries are under heavier scrutiny than others.

In 2024, the agency issued 149 warning letters to human food manufacturers for failing to follow current good manufacturing practices (cGMP) and food safety rules under the Food Safety Modernization Act (FSMA). Another 37 went to animal food companies. These aren’t random. They often follow inspections where inspectors found mold, cross-contamination, or unapproved additives.

Pharmaceuticals are a bigger target. In the first half of 2025 alone, the FDA issued 58 warning letters to compounding pharmacies and telehealth companies selling fake versions of weight-loss drugs like semaglutide and tirzepatide. These companies claim their compounded drugs are “custom-made” but market them like FDA-approved brand-name products - which is illegal. The letters cite violations of Sections 502(a) and 502(bb) of the FDCA, which cover misbranding and false claims.

Tobacco is another hotspot. Since 2021, the FDA has issued over 700 warning letters to companies selling unauthorized electronic nicotine delivery systems (ENDS), especially flavored vapes marketed to teens. Many of these products never went through the agency’s premarket review process, making them illegal to sell - even if they’re popular.

The Enforcement Chain: From Letter to Legal Action

A warning letter is just the beginning. Here’s what happens next:

1. 15-day response window: The company must reply with a detailed plan to fix every issue listed. Vague promises like “we’ll do better” won’t cut it. They need timelines, testing results, and proof of changes.
2. FDA review: The agency checks if the response is credible. If it’s not, they mark the company as non-compliant.
3. Follow-up inspection: FDA inspectors return unannounced to verify fixes. If problems remain, the company is flagged for escalation.
4. Escalation: This can mean anything from a civil penalty of $10,000 to $1 million per violation, to a mandatory product recall, to a formal notice to withdraw product approval.

In extreme cases, the FDA can shut down a facility entirely. For example, if a drug manufacturer repeatedly fails cGMP standards, the agency can revoke its license to produce that drug. Once approval is withdrawn, the product can’t legally be sold in the U.S. again - even if it’s reformulated.

Import Alerts and Foreign Manufacturers

More than 80% of pharmaceutical ingredients and 40% of food products come from outside the U.S. The FDA doesn’t wait for these products to reach store shelves - it stops them at the border.

If a foreign manufacturer has a history of violations, the FDA puts them on an Import Alert. When their products arrive at a U.S. port, they’re automatically detained without physical inspection. The importer has 30 days to prove the shipment is safe. If they can’t, the goods are destroyed or returned.

Since May 2025, the FDA has ramped up unannounced inspections of foreign facilities by 300%. These inspections are now routine for high-risk sites - especially those producing insulin, antibiotics, or infant formula. If a company refuses access, delays inspectors, or redacts documents, they could face criminal charges under Section 303(f) of the FDCA. That’s not a fine. That’s jail time.

What Happens When Companies Ignore the Warning

Some companies think they can wait out the FDA. They don’t. The agency tracks every response. If a company ignores a warning letter or submits a fake corrective plan, the FDA escalates quickly.

One 2024 case involved a telehealth company that sold compounded semaglutide with claims like “FDA-approved” and “better than Ozempic.” Their website had before-and-after photos and patient testimonials - all illegal under FDA rules. After a warning letter, they didn’t respond. The FDA issued a public recall notice, seized all inventory, and referred the case to the Department of Justice. The CEO was later charged with fraud.

Another company, a dietary supplement maker, received a warning for selling products with hidden pharmaceutical ingredients. They replied with a letter saying “we’ve stopped selling those products.” But FDA investigators found the same products still being sold online under a different brand name. The company was hit with a $500,000 civil penalty and a 10-year ban on selling any regulated products.

How to Avoid a Warning Letter

The best way to avoid an FDA warning letter is to stay ahead of the rules. Here’s what compliant manufacturers do:

• Train staff regularly on cGMP, labeling rules, and advertising restrictions
• Keep full, unredacted records - including emails, test results, and supplier contracts
• Don’t make health claims unless they’re backed by FDA-approved data
• Get premarket approval for new products - especially tobacco, drugs, and medical devices
• Work with legal counsel who specializes in FDA compliance - don’t rely on in-house teams alone

Companies that treat compliance as an ongoing process, not a checklist, rarely get warning letters. Those that wait until after an inspection to fix things are already behind.

What’s Coming Next

The FDA’s 2026 budget includes $50 million for more inspectors, better lab testing, and digital monitoring tools. That means more unannounced inspections, more AI-driven analysis of online ads, and faster detection of illegal products sold on Amazon, Instagram, or TikTok.

Expect more warning letters targeting digital marketing. The FDA is now actively scanning social media for misleading claims. A single Instagram post saying “this supplement cures diabetes” can trigger a warning letter - even if the product is technically legal.

The message is clear: the FDA is no longer waiting for complaints or major outbreaks to act. They’re proactively hunting for violations - and they’re not backing down.