Since then, the museum has been caught in a political debate and faced questions about academic freedom and the board’s ties to the Obama administration.

The Times reached out to all 63 museum board members who are presidential appointees or members of Congress, as well as other museum officials. Interviews show that the museum was caught off guard by the impact and furor that its own report would have, and at least some board members were unaware that the museum was wading into a debate about atrocities in Syria.

Leon Wieseltier, a senior fellow at the Brookings Institution and the former literary editor of The New Republic, is among the critics of both the study’s findings and its publication. He said the museum did the right thing by pulling it — a move that was first reported by Tablet magazine.

“The Holocaust museum, if it stands for anything, stands for the idea that we should always act against genocide and that there’s something forever wrong and unsatisfying about the idea that we can do nothing to alleviate radical evil,” Mr. Wieseltier said in an interview. “This paper basically whitewashes the Obama administration’s inaction on Syria and says that there’s nothing we can do.”

That characterization, echoed by other critics, incorrectly describes the report, according to several academics and Syria-watchers. They also said the study’s removal sets a troubling precedent for suppressing independent research.