The op-ed came on the heels of reports based on damning book about Trump's presidency by veteran journalist Bob Woodward and amplified the sense that top advisers to the President have serious concerns about his conduct in office and leadership abilities.
For instance, staff would remove pieces of paper from Trump's desk that they didn't want him to sign, Woodward wrote, and the president wouldn't ask about them later.
The White House, in a statement from press secretary Sarah Huckabee Sanders, dismissed the book as "nothing more than fabricated stories, many by former disgruntled employees, told to make the President look bad".
Trump, appearing at an unrelated event Wednesday at the White House, lashed out at the Times for publishing the op-ed.
In the op-ed titled "I Am Part of the Resistance Inside the Trump Administration", the official said he and like-minded colleagues have vowed to thwart parts of the president's agenda and his worst inclinations. "He complained for weeks about senior staff members letting him get boxed into further confrontation with Russian Federation, and he expressed frustration that the United States continued to impose sanctions on the country for its malign behavior".
"We fully recognize what is happening", the anonymous author said.
But the Times op-ed suggests that dissent and resistance inside Mr Trump's White House are even deeper than Woodward described.
"This is a new low for the so-called "paper of record", and it should issue an apology, just as it did after the election for its disastrous coverage of the Trump campaign", Sanders said.
Melania Trump has accused the author of an anonymous op-ed of "sabotaging" the country.
With Mattis at the Defense Department, "we're having a lot of victories", Trump said.
In the Woodward book, Mattis allegedly said that Trump had the understanding of world and national security affairs of a "fifth or sixth-grader".
Trump responded, saying it was a "gutless editorial" and "really a disgrace", and his press secretary called on the official to resign.
The text of the op-ed was pulled apart for clues: The writer is identified as an "administration official"; does that mean a person who works outside the White House? Trump, the writer argues, holds none of the ideals held dear by conservatives and the Republican Party, adding that the president's impulses tend to be anti-trade and anti-democratic.
The piece led to fierce speculation about who was behind the bombshell, with multiple Trump officials coming out to distance themselves from it. Melania Trump's reaction represented the latest salvo in an aggressive pushback from the White House.
The New York Times said publishing the essay anonymously is "the only way to deliver an important perspective" to its readers.
The erratic behavior would be more concerning if it weren't for unsung heroes in and around the White House.
"I have to say, I'm surprised by how good a writer Ivanka is", he said. The people working aginst Trump while working for him are doing so to ensure the overall success of the administration, the author claims.
"He is not putting the country first, but putting himself and his ego ahead of the will of the American people".