The pharmaceutical industry is finally facing one of its worst-case scenarios: FDA’s drug-safety officials will now hold considerably more sway over both experimental and approved drugs.

Prodded by Congress in the wake of several major drug-safety and effectiveness concerns –  starting, perhaps, with Vioxx, and since expanded to several antidepressants, Avandia, Vytorin, Chantrix and others — the FDA launched a “Safety First” initiative back in February. Although the plan was little more than a vague outline at the time, the good folks at the In Vivo Blog now report that FDA’s Office of Surveillance and Epidemiology will now share equal responsibility over “significant safety issues” with the agency’s power drug-approval office.

The change is momentous because FDA’s safety officers have long played second fiddle to their colleagues in the Office of New Drugs, which industry has long viewed as a more reliable friend than the surveillance office. Public spats between the two arms have grown more frequent since 2004, when FDA drug-safety officer David Graham went public with charges that the agency had long ignored safety problems with approved medicines — most notably the heart-attack risk associated with Merck’s painkiller Vioxx.

Per a memorandum of understanding just obtained by In Vivo, FDA’s safety and drug approval officials will work together in “interdisciplinary teams”  when safety issues arise. More to the point, the surveillance office will take lead responsibility in several areas, including the oversight of safety studies and “medical error prevention.”

If the drug industry needed a clearer signal that its “blockbuster model” of selling drugs to as many people as possible is coming to an end, this shift in regulatory authority is probably it. Of course, there’s no way of knowing in advance exactly how the new process will work out, especially since the two arms of FDA may still end up at loggerheads, despite their insistence that they’ll find ways to reach common agreement.

Whether or not the FDA’s move is the last word, though, drug-safety problems are now a permanent feature of the landscape, since a rise in side effects is an all-but-inevitable consequence of blockbuster-style drug marketing and promotion. The sooner Big Pharma realizes that and acts accordingly, the better.