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The nation’s largest cigarette maker has paid for scientific research at four Massachusetts universities since 2000, a practice that critics of the tobacco industry liken to the Mafia underwriting crime fighting.

Philip Morris USA, which makes Marlboro and other top-selling cigarette lines, gave grants to scientists at Boston University, Harvard University, the Massachusetts Institute of Technology, and the University of Massachusetts, company spokesman David M. Sylvia said Friday.

The research supported by the company touched on conditions such as heart disease and cancer that are linked to smoking. The grants given by the Philip Morris External Research Program were not used to develop new tobacco products or refine existing brands, but they may have helped the company rehabilitate its public image.

When accepting Philip Morris money, the researchers had to promise to disclose the source of their funding in scientific publications, Sylvia said, and the company, in turn, promised not to meddle in the research.

Still, industry foes said research paid for by tobacco companies is irredeemably compromised.

“Taking money from the tobacco industry to conduct scientific research is like the DA taking money from the Mafia to conduct investigations of crime,” said Gregory Connolly, a Harvard School of Public Health professor and former director of the Massachusetts Tobacco Control Program.

University scientists first came under withering attack for taking money from Big Tobacco in the 1990s, when their work was seen as buttressing industry claims that cigarettes were not harmful. The tenor of industry-funded research changed after the companies acknowledged in a landmark settlement in 1998 that their products were lethal.

“Their interest now is to try to convince the public that they are truly concerned companies and that they care enough to fund important research at reputable institutions,” said Dr. Michael Siegel, a Boston University School of Public Health researcher who has extensively studied the tobacco industry. “And, they’re using the good name of these institutions to try to bolster their own scientific and public credibility.”

BU’s acceptance of research grants from Philip Morris was first disclosed Thursday in The Daily Free Press, a student newspaper at the university.

In a statement issued Friday evening, the provost of BU’s medical campus, Dr. Karen Antman, said the school had received $3.99 million from Philip Morris during the past decade and devoted it to the study of tobacco-related diseases.

“We adhere to the highest ethical conduct in research and pursue funding from a variety of sources for unrestricted medical research,” Antman said in the statement. “Our research is conducted and the results are assessed against the standard benchmarks that apply to any research.”

Philip Morris would not disclose how much money in total it distributed through the External Research Program from 2000 through last year, when it was ended. Nor would the company specify the amounts given to Massachusetts scientists.

Worldwide, about 470 research projects were underwritten by the company, Sylvia said, resulting in more than 1,000 publications in journals that subject papers to peer scrutiny, such as the Proceedings of the National Academy of Sciences.

Philip Morris recruited a scientific advisory board to review research proposals, Sylvia said, placing an emphasis on projects related to how smoking causes cancer, heart disease, and respiratory ailments.

“Obviously, cigarettes are a product that is addictive and cause serious disease,” Sylvia said. “Our goal is to try to reduce the harm associated with cigarettes. We felt there needed to be additional research in these various areas to better help us in our effort to reduce the harm related to smoking.”

The company provided three examples of Massachusetts researchers it supported. In two of those cases, the recipients were junior scientists — known as post-doctoral researchers — who often find it difficult to win highly competitive grants from the federal government or other major sources of research support.

One of them said he was happy to get the funding for his work on computer modeling of potential treatments for cardiovascular disease.

“As there were no strings attached in the application process I had no qualms in applying for this funding,” Rami A. Tzafriri, of MIT, said in an e-mail. “In retrospect I can say that the whole process was very professional and friendly and that under similar circumstances I would apply for such funding again. Funding for research is essential, but unfortunately scarce. So any source that does not compromise my independence is welcome.”

MIT officials declined to comment about their researchers’ acceptance of Philip Morris money.

At BU, one recipient, Dr. Douglas Faller, is a longtime professor and director of the BU Cancer Center. According to a document detailing work at the university’s Women’s Health Interdisciplinary Research Center, Faller received $268,759 from Philip Morris to investigate a cancer drug.

Reached at his home late Friday, Faller deferred to university officials for comment.

At Harvard Medical School, researchers were ordered to stop pursuing tobacco-industry grants in July 2004. “The policy did, however, allow those few researchers who had ongoing projects funded by those entities to complete them,” Margaret Dale, dean for faculty and research integrity at Harvard Medical School, said in a statement released Friday by a university spokesman.

When the school issued its policy, administrators acknowledged that grant money can be hard to turn down.

But “in light of the harm that has been caused by the tobacco industry and its products, and considering [Harvard Medical School’s] mission as a leader in teaching, research and patient care,” the only acceptable course was to ban the tobacco grants, the Harvard administrators wrote.

A UMass Medical School spokeswoman said that the school does not currently have any research supported by tobacco companies and that it had accepted “no more than” $2 million from the industry over the past decade. By comparison, she said, the medical school estimates it received a total of $1.3 billion in research funding during that period.

The Tufts University School of Medicine received no Philip Morris grants, but a school spokeswoman said that one laboratory there had received a grant in 2006 from a tobacco company.