"We need to consider this very expeditiously," said Karen Midthun, acting head of the FDA unit that reviews vaccines, as quoted by Reuters.

When would the agency, which isn't exactly known for its speed, act quickly? When pigs fly, would be my guess. But maybe it's actually when pig viruses "contaminate" vaccine.

In March, the FDA recommended that doctors stop using GlaxoSmithKline's (NYSE: GSK) Rotarix -- which protects infants against rotavirus, which can cause fatal dehydration -- after researchers discovered DNA from a pig virus in the vaccine. The porcine virus doesn't seem to be a problem for humans -- or pigs, for that matter -- but the overly cautious FDA decided to issue the recommendation anyway.

Since then, Merck's (NYSE: MRK) Rotateq has had the market to itself, although it hasn't escaped the pig virus issue.

Sales of the rotavirus vaccines aren't at the level of Pfizer's (NYSE: PFE) Prevnar, which vaccinates against strains of Streptococcus pneumoniae, but they aren't too shabby, either. Merck sold $522 million worth of Rotateq last year, while Glaxo managed $440 million from Rotarix. Most of Glaxo's sales occur outside the U.S., but other regulatory agencies might follow the FDA decision.

The FDA convened a panel of experts on Friday to help sort out the mess, but the plot only thickened as Merck said its vaccine also contained parts of pig viruses. No one is quite sure how the viruses got in there, but one component of the manufacturing process uses an enzyme from pigs, so that could be the culprit.

At any rate, FDA advisors seemed to conclude that the risk -- if there is any -- is overshadowed by the benefits of the vaccines.

But the FDA has the final say, and whether this issue can be resolved "expeditiously" remains to be seen. The agency took an extra 10 months to approve Novo Nordisk's (NYSE: NVO) Victoza after a puzzling case of thyroid cancer in rats. Novo Nordisk was stuck in limbo while the agency made up its mind, as were Eli Lilly (NYSE: LLY) and Amylin Pharmaceuticals (Nasdaq: AMLN), the makers of Byetta, which is in the same class as Victoza.

Vaccine makers, especially Glaxo and its currently not-recommended vaccine, certainly hope a decision comes faster than that. 

Let us know what you think in Motley Fool CAPS. Make an out- or underperform call on Merck or Glaxo and post a pitch about whether you think the FDA is being pigheaded. It's free. It's fun. And it's Foolish. 

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