Robert A. Nordin, the pharmacy manager at Gillette Children’s Specialty Healthcare in St. Paul, said his hospital was losing hundreds of thousands of dollars’ worth of discounts on drugs like Botox and Rituxan.

Christina M. Barnes, the pharmacy director at Galion Community Hospital in rural Galion, Ohio, said she was excited when her hospital qualified for the discount program earlier his year. But, she said, she was dismayed to learn that many drugs would be excluded.

“We were given an advantage with one hand, and it was taken away with the other hand,” Ms. Barnes said.

William A. Sarraille, a lawyer at Sidley Austin in Washington who represents drug makers, said, “The discounts are huge and can have a very significant, very negative impact on the ability of manufacturers to develop new, better products that meet patients’ needs.”

The Food and Drug Administration classifies more than 350 medicines as orphan drug products. Manufacturers said they could not recover the costs of developing such drugs if they were required to sell them at deeply discounted prices.

A House Democrat who worked on the health care law said the situation had resulted from “an honest mistake in drafting,” and he added, “No one intended to take away any of the drug discounts that children’s hospitals already had.”

The discount program is widely known as the 340B program, after the relevant section of the Public Health Service Act.