(FORTUNE Magazine) – Johnson & Johnson stock got hammered in mid-July when the government launched an investigation into its plant in Puerto Rico that makes Eprex, a bioengineered medicine sold outside the U.S. to treat anemia. Ironically, Johnson & Johnson's drug had actually caused a rare form of anemia in some people. Meanwhile, at a plant in Boulder, Amgen, the drug's developer, has produced the very same medicine since 1989 under the name of Epogen with only a few cases of severe immune response.

This disparity reveals a burgeoning problem facing generic drugmakers. A common misconception is that once a company has the rights to make a drug, the manufacturing of it is easy. That's not the case. Decades of experience in chemical manufacturing means almost nothing when it comes to bioengineering drugs.

The process is much more complicated than simply copying a pill like Prozac. Biotech companies like Amgen invest several years of work and hundreds of million of dollars in equipment to get new production lines built and approved. The drugs that have come from the biotech revolution are large, complex protein molecules that are produced in a carefully monitored nutrient soup in fermentation vessels called bioreactors. Inside the brewery-like vessels are zillions of genetically modified animal or bacteria cells--for Epogen, Amgen uses Chinese hamster ovary cells, of all things--into which a human gene has been inserted containing the instructions for making the desired protein. Treated just right, the cells will churn out commercial quantities of a drug over a multiweek production run. "We don't really make this protein--we grow it, under a very complicated set of conditions. All these variables have to be precisely right," says Fabrizio Bonanni, Amgen's senior vice president for quality control.

But errors or contamination can easily reduce a bioreactor's contents to junk that must be discarded. Just what caused Johnson & Johnson's Eprex problem isn't clear, but something may have gone awry in its bioreactors. In any case, the lack of clarity about the problem is one reason the Food and Drug Administration is so concerned. When two of the earliest biotechnology products, human growth hormone and insulin, went off patent, the FDA required aspiring generic competitors to launch extensive and expensive clinical trials to demonstrate the safety of their knockoffs.

The bottom line: The Johnson & Johnson imbroglio suggests that copying bioengineered drugs won't be easy. That gives biotechs an edge when competing with generic drugmakers that Big Pharma never had.