James Dao, the newspaper's op-ed editor, said in the Times' daily podcast that while an intermediary brought him together with the author, he conducted a background check and spoke to the person to the point that he was "totally confident" in the identity.
It would look like the Times was trying to stir the pot if it were not a high-level person, said Chuck Todd, host of NBC's "Meet the Press".
In one eye-opening passage, the writer says cabinet members initially considered invoking the 25th Amendment of the US Constitution, which provides for the president's removal if he is "unable to discharge the powers and duties of his office". The @nytimes should be ashamed and so should the person who wrote the false, illogical, and gutless op-ed.
Vice President Mike Pence, Secretary of State Mike Pompeo, Defense Secretary Jim Mattis and Director of National Intelligence Dan Coats were among those who issued denials.
"The Deep State and the Left, and their vehicle, the Fake News Media, are going Crazy", Mr Trump tweeted.
The writer describes the president as "impetuous, adversarial, petty and ineffective".
Getty Melania Trump released a statement on the op ed.
Trump and his inner circle have been in damage control all week fighting similarly themed revelations contained in Pulitzer Prize-winning journalist Bob Woodward's upcoming book, "Fear: Trump in the White House".
Trump has been very upset and vocal about the article.
"But for those who are not true Trump believers, I think it is quite likely that these events will reinforce the Democrats' argument (that) a check on the President is a valid and increasingly urgent necessity for the good of the country".
Anonymous opinion pieces are unusual at the Times, too, but the paper has gone there before - most recently in June, when it published an op-ed by an unnamed Salvadorian asylum-seeker. "To the writer of the oped - you are not protecting this country, you are sabotaging it with your cowardly actions". His deputy chief of staff said Pence's office is "above such amateur acts".
Down Pennsylvania Avenue, House Speaker Paul Ryan said he did not know of any role Congress would have to investigate, though Republican Rep. Mark Meadows of North Carolina, a Trump ally, said the legislative body could take part.
The writer, identified by the Times only as a senior administration official, said that he or she, and others in government, have vowed to thwart the president's "more misguided impulses until he is out of office".
"It seems unlikely to me this person is a holdover when the person is praising the tax cuts - praising deregulation, talking about the fact that they like many things that happened", Berman told the stonefaced Trump defender.