The city health commissioner’s campaign to post calorie information on fast-food and chain restaurant menus may leave the mayor with egg on his face, so to speak.

That is the implication of information turning up in a lawsuit an association of restaurateurs is pressing against the Department of Health and Mental Hygiene. The restaurateurs have unearthed evidence that the Centers for Disease Control and Prevention criticized and rejected the study now being used by the city to defend the new menu regulation, and that a top health department official tried to cherry pick scholars who have previously advocated for the regulation to act as peer reviewers of the study.

A federal judge, Richard Holwell of U.S. District Court in Manhattan, will rule this month on whether the regulation violates what restaurant owners say is their First Amendment right to decide what they put on their menus.

Because Judge Holwell may consider what scientific evidence supports the city’s claim that the regulation will reduce obesity, the health department’s study is emerging as a key element of the city’s defense of the regulation.

The initiative fits into Mayor Bloomberg’s program of forcing New Yorkers into healthier lifestyles.

More broadly, the dispute highlights the pressure New York City is under to get scientific validation for even a relatively minor regulation. If new regulations come under challenge in court, there is always the prospect that judges will accept the findings published in reputable scientific journals.

The study at issue, authored by the health commissioner, Thomas Frieden, and a deputy commissioner, Mary Bassett, among others, grew out of a survey last year of more than 7,000 purchases at a variety of fast food restaurants. The authors focused on Subway — which was then the only fast-food restaurant voluntarily displaying calorie information on its menu boards — and found that patrons who noticed the calorie information were likely to purchase a meal containing 51.7 fewer calories. Only a third of the customers reported noticing the calorie counts.

City health officials ran into difficulties at the end of last year when they tried to get the report published. The editor at the Morbidity and Mortality Weekly Reports, published by the CDC, wrote in an e-mail message to Dr. Frieden that the “conclusions being drawn by the study, are of course, problematic.”

One problem identified by the editor, Frederic Shaw, was the focus on Subway, which uses an ad campaign about weight loss and may attract a more calorie-conscious clientele, according to an email sent by Dr. Shaw to Dr. Frieden. More broadly, Dr. Shaw suggested that there was “a lurking probability that people who look at caloric information are much different from everybody else.” In other words, many people may not change their eating habits despite being confronted with data. Dr. Shaw ended the e-mail by saying that he was “very impressed with what you are trying to do in NYC with obesity” even though it means “taking some unpopular stands.”

In January, Dr. Frieden responded: “We don’t agree on your critique — but we can agree to disagree.”

The e-mails were recently obtained by the restaurant association and are now a part of the court record. In a letter to the court, a lawyer for the New York State Restaurant Association faulted the agency for not telling the court earlier that the study had been rejected for publication by both the CDC and the Journal of the American Medical Association. The lawyer, Kent Yalowitz of the firm Arnold & Porter, also suggested that Dr. Bassett, the deputy commissioner, should have disclosed “her personal involvement in recruiting peer reviewers to review the study of which she was the lead author.” Mr. Yalowitz never explicitly accuses Dr. Bassett of a conflict of interest, but does suggest that the city was in a rush to get the study published so that it could cite it in the current litigation.

In an interview, Dr. Frieden said there was nothing improper about trying to publish quickly in order to get out ahead of the restaurant association’s lawsuit, which the agency anticipated.

“Medical researchers want to get their research out in time to effect policy,” Dr. Frieden said. After two rejections, Dr. Bassett turned to a journal of which she is an associate editor, the American Journal of Public Health. In a January e-mail message to the top editor, Mary Northridge, Dr. Bassett said she hoped the journal would move quickly in considering the piece. “We really want it published or at least accepted, in time for what we expect is coming — another suit,” the e-mail said. Both Dr. Northridge and Dr. Bassett have appointments at the Mailman School of Public Health at Columbia University.

Dr. Bassett next turned to two experts in the field of public health and nutrition, Marion Nestle of New York University and Kelly Brownell at Yale, and asked them via e-mail whether they could peer review the study during the journal’s vetting process. Both had already filed court briefs on behalf of the city’s regulation the year before, in a previous round of litigation, Mr. Yalowitz noted in his letter.

The peer review process at the journal is supposed to take place anonymously, with the reviewers and authors unaware of each other’s identity. However, the journal does ask authors to recommend several names of potential peer reviewers familiar with the field.

Responding to questions from The New York Sun, Dr. Northridge wrote in an e-mail message that neither Dr . Brownell nor Dr. Nestle ended up serving as peer reviewers. She would not disclose who did, citing the journal’s peer review policy. The study is slated to be published in August, but the city has already cited it several times in the court record.

Asked by the Sun whether his court brief in support of the regulation ought to prevent him from peer reviewing the city’s study, Dr. Brownell wrote via e-mail: “I would consider it a legitimate question and would not review an article under such conditions.”

In an interview, Dr. Bassett said that the number of qualified peer reviewers on the topic was limited and that she sought out Dr. Brownell and Dr. Nestle for their expertise.

“We were looking for people who have academic credibility,” Dr. Bassett said. “Those may also be the same people who have been willing to lend support to our policy initiative.”

The regulation requires both fast food restaurants and restaurants with more than 15 locations nationwide to display calories on either menu boards or menus.