It isn’t Mayor Bloomberg’s best-known health crusade. But while he gets blocked on soda cup sizes, the data magnate has been a national leader in encouraging doctors to ditch pen and paper and computerize their patients’ files.

Now new research is in on New York City’s pioneering push in electronic health records, and the results are mixed.

A recent study in the journal Health Affairs tracked 360 doctors participating in NYC REACH — a city-sponsored program that since 2005 has received more than $85 million in government funds and reinvested $30 million to get doctors plugged in.

The program subsidizes software costs for practices making the switch from paper to electronic records. It serves as an information hub connecting physicians with technical support services, from hardware installation to coaching on how to use the systems.

The theory behind the technology holds that digitizing patients’ medical records lowers costs while improving care. Electronic health records systems ping doctors when they prescribe a medication that reacts with a drug the patient is already on and prompt physicians to discuss preventive services, like breast cancer screenings and urine tests for diabetics. If a problem is spotted before it starts, the thinking goes, the healthier patients will end up.

Yet the study found that the practices of doctors who adopted the technology, largely in medically underserved neighborhoods, by and large did not see improvements in quality.

One reason was that the doctors and their staff didn’t get enough technical support. Offices needed eight or more visits from specialists to troubleshoot system problems and train staff on the software before any health care quality measures improved. But nine out of ten practices in the study had far fewer; the average was around three.

And even at the small minority of practices that cracked the code, the only improvements came in the number of screenings for certain conditions — like breast cancer and chlamydia screenings — and preventive measures, such as urine testing for patients with diabetes.

“This finding stands in contrast to widespread physician perceptions that EHR improve quality of care,” wrote authors Andrew Ryan and Sarah Shih. Ryan is a professor of public health at Weill Cornell Medical College, and Shih runs program evaluation and planning at the Primary Care Information Project — the bureau within the city’s health department in charge of NYC REACH.

Consultants helping push the technology say doctors and staff at many practices, especially tiny offices running on tight margins, have had a hard time using the system.

“At small practices, say with one to five physicians, everyone has to carry their own weight, and many of them feel like they can’t block out the time,” said Dr. Sal Volpe, chairman of the state Medical Society’s health information technology task force and clinical consultant to the Primary Care Information Project. Low reimbursement rates and hectic schedules, he says, are among the culprits.

“A lot of doctors are like hamsters running on the wheel, as soon as they get in to work they are on the wheel and run — I have to see this many people a day, get on this many calls, interact with subspecialists,” he said. “They literally don’t have the time to think about it.”

The systems also don’t come cheap. Costs for hardware, tech support and training sessions for doctors and staff can exceed $50,000 for a small practice, even with the city program’s help.

Such challenges went largely unmentioned at a February event at the New York Institute of Technology, where Mayor Bloomberg honored the 3,200 doctors around the city who have so far taken the plunge into electronic health records with the help of NYC REACH. The mayor praised the switch to electronic records as an important advance for patients’ health.

“EHRs are helping doctors save thousands more lives by improving preventive care,” said Bloomberg at the event. From 2009 to 2011, he informed the crowd, participating physicians provided preventive services at a rate almost three times higher after starting on the records systems, helping 235,000 people better manage their chronic health problems or quit smoking.

“Every year, hundreds of thousands of people needlessly die from heart disease, stroke, cancer and infections. And we can stop many of those tragedies with EHRs,” said Bloomberg.

Joining Bloomberg for the event were two administration alumni who are now in key roles pushing the technology for the Obama administration. Dr. Thomas Frieden, former city Department of Health and Mental Hygiene commissioner, now heads the U.S. Centers for Disease Control. And Dr. Farzad Mostashari, a lead architect of NYC REACH under Frieden, is now the health information technology czar for the U.S. Department of Health and Human Services.

Led by Dr. Mostashari, the Obama administration has paid out more than $12 billion in incentives to physicians and hospitals nationwide for adopting electronic health records, with billions more to follow. New York State facilities and doctors have received about $640 million so far.

The funds are going out the door while the research is still coming in. The Department of Health and Mental Hygiene provided a summary of the research cited by the mayor, showing a higher rate of preventive care for patients with electronic records. It would not share the paper it’s based on, which has yet to be peer-reviewed.

The current assistant commissioner in charge of REACH, Jesse Singer, penned an op-ed in Health Affairs in response to Ryan and Shih’s study, touting the unrealized promises of electronic health records , but did not cite the rosy numbers quoted by the mayor.

Ryan isn’t sure how the mayor knows how patients fared. “Absent any detail for how those numbers were generated, personally knowing how difficult it is generate estimates of the effect of policies, and knowing that the city has little or no data from providers that were not part of PCIP, I would be skeptical of the conclusion that PCIP had no effect of process measures but had a huge effect on outcome measures,” said Ryan.

Yet even without consistent data supporting their ability to improve health care, use of electronic health records has ballooned. More than two-thirds of family doctors nationally in 2011 used the technology, double the share who did in 2005.

Much of the cost of expansion — by one estimate, totaling $1 trillion — is falling on government. The rapidly growing electronic health records industry is expected by some to be worth $6 billion by 2015, in a boom that has led to scrutiny of profits and executive salaries in the health information technology industry, largely financed through federal incentives.

The past few months have also seen a tempering of initially high expectations. The RAND corporation walked back a 2005 study that predicted electronic health records would save the government some $81 billion annually while improving care, though the authors held that the hopes can still be fulfilled.

The hope stems from the relative handful of systems that work well — like at Essen Medical Associates, a five-facility, 40-provider network headquartered in Morris Heights in the Bronx. Medical director Dr. Sumhir Sahgal said the health-records technology has made his job easier, made workers and patients happier and tangibly improved the way he cares for patients.

Sahgal pointed to a new diabetes screening technique, which he has found keeps 97 percent of his more than 1,000 pre-diabetic patients from converting to full diabetes within the year. Studies have shown the average conversion rate to be between 4.5 and 10 percent.

He said prompts on the side of the computer screen spare him from having to dig through piles of patients’ records to find clues about their medical history, making conversations about treatments and preventive measures more efficient.

“Now communication is so much faster; we can be proactive,” he said. “And no one has to read my handwriting.”

It took a lot of pain to get where he was. During the first six months, Sahgal had to spend so much time inputting medical records into the unfamiliar system that he could only see between seven and 10 patients a day, when he could usually help around 25. He and his staff would stay late into the night to keep on top of their workload.

All in all, he had to spend more than $60,000 — only a fraction of which was subsidized by REACH — to buy the hardware and software, and all the support needed to run it properly. He estimated that during the first six months he arranged a dozen or so on-site trainings and another 10 visits for tech troubleshooting and installation.

But he remains convinced that the progress was worth all the trouble.

“By a year out we looked back and thought, ‘this is great,’” he recalled. “Two years later we looked back and thought, ‘how did we practice before’?”