A research director for Pfizer was positively buoyant after reading that an important medical conference had just featured a study claiming that the new arthritis drug Celebrex was safer on the stomach than more established drugs.


“They swallowed our story, hook, line and sinker,” he wrote in an e-mail to a colleague.


The truth was that Celebrex was no better at protecting the stomach from serious complications than other drugs. It appeared that way only because Pfizer and its partner, Pharmacia, presented the results from the first six months of a yearlong study rather than the whole thing.


The companies had a lot riding on the outcome of the study, given that Celebrex’s effect on the stomach was its principal selling point. Earlier studies had shown it was no better at relieving pain than common drugs — like ibuprofen — already on the market.


The research chief’s e-mail, sent in 2000, is among thousands of pages of internal documents and depositions unsealed recently by a federal judge in a long-running securities fraud case against Pfizer. While the companies’ handling of the research was revealed a dozen years ago, the documents provide a vivid picture of the calculation made by Pfizer at the time and its efforts ever since to overcome doubts about the drug.


The documents suggest that officials made a strategic decision during the early trial to be less than forthcoming about the drug’s safety. They show that executives considered attacking the trial’s design before they even knew the results and disregarded the advice of an employee and an outside consultant who had argued the companies should disclose the fact that they were using incomplete data.


In one e-mail, an associate medical director at Pharmacia (which was later bought by Pfizer) disparaged the way the study was being presented as “data massage,” for “no other reason than it happens to look better.”


In another, a medical director at Pfizer described it as “cherry-picking the data” even as officials were publicly boasting of the study’s success. Dr. M. Michael Wolfe, a gastroenterologist who had cautiously praised the study in a medical journal at the outset, said after reviewing the new documents: “I always try to give investigators the benefit of the doubt, but these communications make it quite challenging for me.”


The importance of Celebrex to Pfizer is indisputable. It is one of the company’s best-selling drugs, racking up more than $2.5 billion in sales, and was prescribed to 2.4 million patients in the United States last year alone.


The drug is the last of the so-called COX-2 inhibitor pain drugs, after Vioxx and Bextra were withdrawn in 2004 and 2005 because of safety concerns.


Some of the Celebrex’s detractors contend that its risks are still not fully understood, and argue that Pfizer is dragging its feet on a study — now nearly six years old — evaluating the drug’s heart risks. The study is scheduled to end in May 2014, the same month that Celebrex loses its patent protection and sales of the drug are expected to plunge.


Then and now, Pfizer has defended its decision to release partial results from the 2000 study and denies any intent to deceive. Company officials have said the drug has demonstrated its worth and safety. The proof, they say, is that 33 million Americans have taken it. “The bottom line is Celebrex is a very important option for many of these patients,” said Dr. Steve Romano, head of the medicines development group in Pfizer’s primary care unit.


The decision by Pfizer and Pharmacia to withhold crucial data became widely known in 2001, after the Food and Drug Administration released the study’s full results. The revelations, along with similar reports of withheld data by other drug companies, led to calls for reforms in the way data from clinical trials is published, including in The Journal of the American Medical Association, which ran an article featuring the partial results from the study.


The withheld data also led to a lawsuit, filed in 2003, by several pension funds that charged that by handling the results the way they did, Pfizer and Pharmacia had misled investors and were responsible for a drop in Pharmacia’s stock value when the full results were revealed.