Why the Flu Vaccine Shortage?

The best explanation I've seen so far is by Alex Tabarrok at Marginal Revolution here and here. He mentions several culprits for the current shortage of flu vaccine.

1. Liability risk. Producers of vaccines are subject to litigation.
2. FDA regulations and requirements. These regulations are often costly, and reduce the profitability to producers.
3. Price controls. The federal government is a major purchaser of vaccines and uses its monopsyny power and/or the law to force low prices, creating a disincentive to produce.

So, it seems well-founded to say that government regulation and control have led to the current shortage, at least indirectly.