The report said that Michael D'Andrea was recently named as the chief of Iran operations and described him as having the most responsibility in "weakening al Qaeda."
Major publications typically do not reveal the identities of undercover agents, but the Times reasoned that it was fair to name D'Andrea because "his identity was previously published in news reports, and he is leading an important new administration initiative against Iran."
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The conservative Federalist website took exception with the second half of that. "So the Times has apparently made it the newspaper's mission to make the agency's work much more difficult and far more dangerous by publicly identifying the man in charge of its covert operations in the Persian country," the group said.
The news reports in which D'Andrea was previously identified in includes a Times article in 2015, in which he was described as central to the Obama administration's drone strike program.
The Times also rationalized its decision for naming D'Andrea in 2015.
"The C.I.A. asked that Mr. D'Andrea's name and the names of some other top agency officials be withheld from this article," the paper said at the time, "but the New York Times is publishing them because they have leadership roles in one of the government's most significant paramilitary programs and their roles are known to foreign governments and many others."