“In an average year over the 10-year period, per-capita refugee costs for major H.H.S. programs totaled $3,300,” it says. “Per-person costs for the U.S. population were lower, at $2,500, reflecting a greater participation of refugees in H.H.S. programs, especially during their first four years” in the United States.

It was not clear who in the administration decided to keep the information out of the final report. An internal email, dated Sept. 5 and sent among officials from government agencies involved in refugee issues, said that “senior leadership is questioning the assumptions used to produce the report.” A separate email said that Mr. Miller had requested a meeting to discuss the report. The Times was shown the emails on condition that the sender not be identified. Mr. Miller personally intervened in the discussions on the refugee cap to ensure that only the costs — not any fiscal benefit — of the program were considered, according to two people familiar with the talks.

He has also played a crucial role in the internal discussions over refugee admissions, which are capped by an annual presidential determination that is usually coordinated by the National Security Council and led in large part by the State Department.

This year, officials at the State Department as well as the Department of Defense have argued vociferously that the United States should admit no fewer than the 50,000-refugee cap that Mr. Trump imposed in January as part of the travel ban, but Mr. Miller has advocated for a much lower number — half or less, according to people familiar with the internal talks who described them on condition of anonymity because they were not authorized to detail them. The Department of Homeland Security last week proposed a cap of 40,000. The limits being debated would be the lowest in more than three decades.

“We see an administration that’s running a program that it’s intent on destroying,” said Mark Hetfield, the president of HIAS, one of nine refugee resettlement agencies opposing the cut in admissions. “We do have champions in the White House and in the administration, but they’re not being given a voice in this.”

The issue is coming to a head as Mr. Trump attends the United Nations General Assembly this week for the first time as president. The United Nations has repeatedly appealed to nations to resettle 1.2 million refugees fleeing war and persecution from all over the world, and former President Barack Obama used the gathering last year to tout his goal of admitting 110,000 refugees in the fiscal year that ends this month, and to pressure other countries to follow the lead of the United States in embracing more displaced people.