“From our perspective, this does bring to light a public health concern, but for a different reason,” said Kimberly Martinez, the executive director of the Abstinence Clearinghouse, which advocates abstinence from sex until marriage. “These young women are relying on this contraception to protect them. But contraception isn’t 100 percent — for pregnancy or for disease.”

The price change came as part of the tangled method by which drug manufacturers pay rebates to states for prescription drugs covered by Medicaid, the federal drug program for low-income people. Those rebates are set by calculations that take into account the lowest prices paid for certain drugs. Since 1990, the steeply discounted contraception given to university health centers and low-income clinics was considered exempt from those calculations.

The arrangement helped those who could least afford the contraceptives to receive them, but was also seen as potentially beneficial to drug companies, which might not make money on the college clinic sales but were able to market their products to young women who might grow accustomed to one brand over another.

More recently though, legislators, worried about abuse in the rebate calculations, set strict limits about which facilities would be exempt. Student health centers, among others, were left out — an unintended oversight, some lawmakers now say.

Image Katie Ryan, a senior at the University of North Dakota, says the monthly cost of her birth control has jumped to nearly $50 from $12. Credit... Eric Hylden for The New York Times

The new rules, part of the Deficit Reduction Act of 2005, came into effect at the start of this year, prompting pharmaceutical manufacturers to tell college clinics that they could no longer afford the huge discounts. Knowing that the change was coming, many health clinics stocked up on the discounted prescriptions and were able to offer cheaper contraception for months, into the summer and even the fall.

Then prices began skyrocketing.

“What happened here is what happened everywhere: The price went up,” said Jeanne Galatzer-Levy of the University of Illinois at Chicago. “We are a state institution, so we’re not in a position to do something different.”