The department’s leaders rejected the staff’s finding. An unpublished draft of the E.P.A.’s upcoming soot rule, viewed by The New York Times, proposes leaving the current standard in place. The E.P.A. administrator, Andrew R. Wheeler, placed “little weight on quantitative estimates” of the mortality risk associated with fine soot pollution, the draft says.

A final version of the report, published in January to preview the still-unpublished rule, does say the rule as it stands contributes to 45,000 deaths annually, but it also says only that tightening it would reduce “health risks,” not deaths.

An E.P.A. spokeswoman, Corry Schiermeyer, said the numbers inserted into the draft report should not be given much weight. “Draft documents of any kind are preliminary by their very nature, with the content subject to change based on internal reviews, scientific peer review, interagency review, and public notice and comment,” she said.

But lawyers say the data in the September draft may have proven useful for environmental lawyers.

“This document represents the best science and scientific judgment that these particles are deadly at the current level, so judges will give great weight to that science,” said John Walke, a lawyer with the Natural Resources Defense Council.

Mr. Walke said that he learned from E.P.A. employees that the scientists had made sure those numbers were published in the document. “People were stunned that this document was even allowed to come out,” he added.

Many federal employees who work on health, science and environmental policy, who spoke anonymously for this story, described using facts in the fight to keep their previous work alive.

Margo Oge, who resigned from the E.P.A. in 2012 after 32 years at the agency, most recently as the head of its office of vehicle emissions policy, said she has advised former colleagues who cannot leave their jobs, “hold your nose and do your best. There may be opportunities where you can impact some of the data that will be used in these rulemakings.”