When Heather Dougherty heard the news last week that the Food and Drug Administration had recommended tightening how doctors prescribed the most commonly used narcotic painkillers, she was overjoyed. Fourteen years earlier, her father, Dr. Ronald J. Dougherty, had filed a formal petition urging federal officials to crack down on the drugs.

Dr. Dougherty told officials in 1999 that more of the patients turning up at his clinic near Syracuse were addicted to legal narcotics like Vicodin and Lortab that contain the drug hydrocodone than to illegal narcotics like heroin.

Since then, narcotic painkillers, or opioids, have become the most frequently prescribed drugs in the United States and have set off a wave of misuse, abuse and addiction. Experts estimate that more than 100,000 people have died in the last decade from overdoses involving the drugs. For his part, Dr. Dougherty, who foresaw the problem, retired in 2007 and is now 81 and living in a nursing home.

“Too many lives have been ruined,” his daughter said.

The story behind the F.D.A.’s turnaround on the pain pills, last Thursday, involved a rare victory by lawmakers from states hard hit by prescription drug abuse over well-financed lobbyists for business and patient groups, one that came during a continuing public health crisis.

Just last year, Representative Fred Upton, Republican of Michigan — the House’s biggest recipient during the last election cycle of drug industry campaign contributions, withnearly $300,000 — blocked a measure that would have imposed the restrictions the F.D.A. backed last week.

Among the provisions in the bill, pushed by Senator Joe Manchin III, Democrat of West Virginia, was one that is central to the new F.D.A. recommendations: reducing to 90 days the length of time in which a patient could obtain refills for painkillers containing hydrocodone without a doctor visit. The drugs are now widely sold by generic producers.

Mr. Upton, who is the chairman of the House Energy and Commerce Committee, argued that imposing new limits would harm patients who needed the drugs, which are used to treat pain from injuries, arthritis, dental extractions and other problems. That stance was echoed by patient groups, lobbyists representing drug makers, pharmacy chains like Walgreens and CVS, local drugstores and physicians groups like the American Medical Association.

The F.D.A.’s long resistance to added restrictions on the drugs underscores what critics say is its continuing struggle to address the complexities of the painkiller problem in its often conflicting roles — one as a regulator that approves drugs and the other as a drug safety watchdog.

On Friday, public health advocates who had cheered the agency’s decision the day before were dismayed when the F.D.A. approved a new, high-potency painkiller despite an 11-2 vote by an expert panel of its own advisers not to do so. The panel concluded in December that the long-acting opioid, called Zohydro, could lead to the same type of abuse and addiction as OxyContin.

A top F.D.A. official, Dr. Douglas Throckmorton, said Zohydro would give doctors another drug to treat long-term pain. But Representative Harold Rogers, Republican of Kentucky, said on Friday that top F.D.A. officials had recently assured him they would only approve new opioids like Zohydro if they were marketed in formulations intended to deter abuse. OxyContin is now formulated that way, but Zohydro, which is contains hydrocodone without acetaminophen, is not. Its producer, Zogenix, says it will closely monitor use of the drug.

“It is like the original OxyContin, so that is real problematical,” Mr. Rogers said.

It was in 1999 that Dr. Dougherty noticed there was something unusual about the regulations governing the pain pills to which his patients were becoming addicted.

Hydrocodone, the active narcotic in the pills, faced tighter prescribing restrictions if used alone than if it was contained in a medication that combined it with acetaminophen, an over-the-counter painkiller found in products like Tylenol.

Controlled substances are overseen by the Drug Enforcement Administration, which classifies drugs and their prescribing rules into categories called schedules based a medication’s potential for abuse. In the 1970s, drug companies successfully argued to Congress that Vicodin and similar products should be placed in a less restrictive category known as Schedule III because the use of over-the-counter drugs like acetaminophen in them would reduce their misuse and increase their effectiveness.

Schedule III drugs are easier for doctors to prescribe and for patients to refill than those considered to pose the highest abuse risk, which are placed in Schedule II. For example, patients can get refills for a Schedule III drug for as long as six months before seeing a doctor again, twice as long as for a Schedule II drug. Also, drugstores face tighter and more costly storage and record-keeping requirements for Schedule II drugs.

By the 1980s, however, drugs like Vicodin were being widely abused, and when Dr. Dougherty petitioned D.E.A. officials in 1999 urging a crackdown, the number of overdose deaths was also climbing.

The D.E.A. began a lengthy investigation, and the agency called on the F.D.A. in 2004 to undertake a review. “Law enforcement has documented the diversion of millions of dosage units of hydrocodone by theft, doctor shopping, fraudulent prescriptions, bogus call-in prescriptions,” D.E.A. officials wrote at the time.

The F.D.A. concluded in 2008 that the pain pills should remain in Schedule III. It argued that the drugs were less prone to abuse and that indicators of problems associated with them, like increased emergency room visits, were, when viewed on a relative basis, not as high as for Schedule II drugs because the pills at issue were prescribed far more often.

Experts said there was actually little clear data on either side. For one, scant testing existed on the question of whether acetaminophen lowered hydrocodone’s abuse. And data about the drugs’ effect in the real world, like hospital visits, was imprecise and could be interpreted in different ways.

“It made no sense that these were Schedule III drugs,” said Dr. Edward Michna, a pain expert at Brigham and Women’s Hospital in Boston.

But there were other issues besides scientific ones. Lobbying groups representing interests like drugstores and patient organizations like the American Cancer Society had long argued that changing the medication’s scheduling would have broad patient effects and that other steps could be taken to curtail the drugs’ abuse. Such patient groups receive drug company contributions, and while they insist those do not influence their policies, they often join lobbying forces with drug companies on issues related to access to medications. Amid the debate, some lawmakers tried to take action.

Before joining the Senate in 2010, Mr. Manchin, as governor of West Virginia, had watched the devastation caused by prescription painkiller abuse. “Doctors are passing out this drug like candy,” he said.

He came to Washington determined to change things. But last year he witnessed the influence of the drug industry when Mr. Upton, the representative from Michigan, after receiving appeals from pharmaceutical industry executives and other groups to intervene,blocked the proposal that Mr. Manchin had persuaded the Senate to adopt.

A spokeswoman for Mr. Upton said he believed Congress should not be micromanaging agencies.

“Drug scheduling requires the expertise of the F.D.A. and D.E.A.,” that spokeswoman, Noelle Clemente, said. “This decision should be made by the agencies.”

Mr. Manchin, however, salvaged what then appeared to be a minor concession, a requirement that the F.D.A. hold a public hearing to review the issue.

When the meeting began in January, it appeared that a panel of outside F.D.A. advisers would side with the view of agency scientists that there was not enough evidence to warrant action, said Sharon Walsh, a researcher at the University of Kentucky who was invited by the agency to give a presentation. But as the day unfolded, she said, the position of those experts appeared to shift as they reviewed the data and heard compelling testimony both from parents who had lost children to drug abuse and patients helped by the medications.

At the end, the panel voted 19-10 to tighten prescribing controls. But such votes are not binding on the F.D.A.

As months passed, Mr. Manchin feared lobbyists on the other side would prevail, as they had on his legislative proposal.

“I was getting worried that K Street was about to block this again,” he said, using the Washington vernacular for lobbyists.

So he began a counterattack and, in recent weeks, contacted top officials at the White House, the F.D.A. and the Department of Health and Human Services. He also enlisted other lawmakers like Senator Tom Harkin, Democrat of Iowa, to make calls to top Obama administration officials.

On Thursday, both he and Mr. Upton received phone calls from top health officials, notifying them of the decision.

“It is still nice to know that good things can be done,” Mr. Manchin said.

Still, experts said, some patients, like those who live in rural areas or are homebound or innursing homes, would face new hardships in obtaining the drugs under the new rules. They added that doctors might turn to less effective drugs.

On Saturday, Dr. Dougherty’s daughter visited her father and shared the news. His eyes brightened and he tried to sit up in bed, she said.

“It was a long time coming, wasn’t it, Dad?” she said.

“Yes, it was,” she said he replied.