"It's not a new position for (Trump). The fact that he reiterated his position again made investors nervous about his position on price controls. ... Outside of the comments he's made about drug prices there's so much uncertainty about the (Affordable Care Act) and what the Trump administration could do," Loo said.
During the election campaign, Trump's health-care platform highlighted the need to negotiate drug prices.
Among the largest decliners midday Wednesday were Celgene, down about 5 percent, Illumina, off about 3.5 percent, and Amgen and Biogen, down 2 percent.
However, Chris Meekins, research analyst on health policy at FBR, said investors should "ignore Trump drug prices comments."
Meekins said in a Wednesday note that Tom Price, Trump's pick to head the department of Health and Human Services, and the Republican-controlled Congress would not support government regulation on drug prices. Meekins also said Trump's comments were more of a negotiation tactic than an indication on policy.
Health-care stocks were among the top performers immediately after the election. The IBB biotech ETF surged then for its best week ever, after being pressured all year by expectations of a Clinton election win and government crackdown on high drug pricing.
Other analysts were quick to support the idea that Wednesday's biotech sell-off was overdone.
The president-elect's tax priorities "should provide growth opportunities" for the biotech sector, said Ying Huang, U.S. biotechnology analyst at Bank of America Merrill Lynch. The case for biotech is bolstered, he said, by cuts in corporate tax rates and efforts to give tax breaks for corporate cash held overseas.
Trump wants to lower the corporate rate to 15 percent; Huang said biotech companies collectively pay an effective tax rate of 20 percent. On the corporate cash side, biotech firms have $84 billion of cash on hand, $69 billion of which is being held overseas.
"We expect political pricing pressure to fade and tax reform and repatriation to provide growth opportunities," Huang said.
In response to the Trump comments published in Time, the U.S. drugmakers trade group, PhRMA, said in a Reuters report that government mandates and interventions are not the right means of addressing prescription drug costs.
— CNBC's Jeff Cox and Meg Tirrell contributed to this report.