Some of the difference in prices is the result of actions taken by pharmacy-benefit managers like CVS Health, which manage drug plans for insurers. They have become more sophisticated in recent years, leading to better discounts from drug companies. They cite successes like the major discount that Gilead, the maker of an expensive new hepatitis C drug, conceded after AbbVie released a competing product. And sales of expensive new cholesterol-lowering drugs, called PCSK9 inhibitors, have been sluggish, in part because insurers have placed numerous restrictions on their use.

“I think we’ve upped our game,” said Dr. Troyen Brennan, chief medical officer of CVS Health. “It’s much more dynamic and much more fast-paced, and I think that like us, the other P.B.M.s are responding much more rapidly.”

So if drug makers’ list prices aren’t representative of the true cost of a drug, why risk negative publicity by raising them? Many rebates and other discounts are tied to a percentage of the list price, which means a higher list price still yields more profit. And not every insurer and pharmacy-benefit manager is as sophisticated as the top players, so manufacturers can profit on the margins.

“The structure of the system is such that the only way they can get any increase in prices is to raise the list price by a very high percent,” said Mr. Fein. “It’s kind of baked into the system, and it’s so complicated, you can’t really unwind it without blowing up the entire health care system.”

Some of the most recent price increases may also be happening because drug makers are hoping to profit while they can, before congressional or other actions prevent them from doing so, said Geoffrey Porges, the author of the Leerink analysis.

“When you see this type of very aggressive pricing action across many products, then you start to scratch your head and say, is this the industry preparing for a more challenging price environment?” he said. “There’s just a general fear of the unknown.”