The Food and Drug Administration's warning system is getting out of control. At some point, a company will get hurt by the agency's rabid warnings -- and take its investors down with it.

Earlier this month, the agency warned that Johnson & Johnson's (NYSE: JNJ) Benadryl Extra Strength Itch Stopping Gel shouldn't be taken internally. The agency's solution? Make Johnson & Johnson change the packaging so that the words "For Skin Use Only" are more prominent, and tell the company to undertake studies to "better understand factors that may contribute to consumers mistakenly swallowing" the gel. Um, maybe it's because they couldn't be bothered to read the label. I doubt that a new label with bigger words will help anyone avoid a date with the Darwin Awards.

Then yesterday, the agency slapped a warning about liver toxicity on Roche's prescription weight-loss drug, Xenocal, and its over-the-counter little brother, Alli, sold by GlaxoSmithKline (NYSE: GSK). A whopping 13 people have reported liver issues out of 40 million who have taken either Xenical or Alli. Granted, not everyone reports adverse events to the FDA, but we still have to be close to the expected range of liver problems for overweight people, whether they're taking weight-loss drugs or not.

In both instances, the warnings aren't likely to cost the companies that much money. But how long will it be until the agency steps over the line from cheaply absurd to costly absurd? Maybe it already has: The agency did turn down Glaxo and XenoPort's (Nasdaq: XNPT) restless leg syndrome treatment Horizant earlier this year, after it seemed to increase pancreatic cancer in rats. Yet the active ingredient in the drug has been on the market for years, as Neurontin from Pfizer (NYSE: PFE).

The wonkiness of the FDA's actions makes it hard for investors to figure out what the agency will do. Investors in Novo Nordisk (NYSE: NVO) sat for months wondering whether the FDA would approve its diabetes drug Victoza, even though the drug seems to cause thyroid cancer in rats. And investors are still nervous about how pancreatitis seen in patients taking Amylin Pharmaceuticals (Nasdaq: AMLN) and Eli Lilly's (NYSE: LLY) Byetta will affect the approval of its long-lasting follow-up, Bydureon.

Obviously, the agency has to do its job and make sure unsafe drugs stay off the market. But this Fool would appreciate it if the FDA would spend more time getting drugs approved, and less time worrying about idiots who swallow topical medications and rare side effects that might not even be real.

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Pfizer is a Motley Fool Inside Value pick. Johnson & Johnson is an Income Investor selection, and Motley Fool Options has recommended buying calls on the stock. Try any of our Foolish newsletter services free for 30 days.

Fool contributor Brian Orelli, Ph.D., doesn't own shares of any company mentioned in this article. The Fool owns shares of GlaxoSmithKline and has a disclosure policy.