"The root of the problem," the author writes, "is the president's amorality. Anyone who works with him knows he is not moored to any discernible first principles that guide his decision making."
In a statement, the White House accused the author of being a "coward" and called on the writer to resign.
"He is not putting country first, but putting himself and his ego ahead of the will of the American people. This coward should do the right thing and resign," the statement said.
Trump frequently rails against the use of anonymous sources, most recently last week, when he tweeted. "When you see 'anonymous source,' stop reading the story, it is fiction!"
In explaining its decision, the Times wrote atop the column, "We believe publishing this essay anonymously is the only way to deliver an important perspective to our readers."
One of the more striking passages in the column refers to the 25th Amendment, which provides a means by which a president who is incapable of fulfilling the duties of the presidency can be removed from office, and the vice president can assume the presidency.
"Given the instability many witnessed, there were early whispers within the cabinet of invoking the 25th Amendment, which would start a complex process for removing the president. But no one wanted to precipitate a constitutional crisis. So we will do what we can to steer the administration in the right direction until — one way or another — it's over."
And while the op-ed is unlikely to change the opinion of Trump's biggest supporters, it could hardly have come at a more inopportune time for the White House.
Trump and his allies on Wednesday were still reeling from the publication on Tuesday of excerpts from Washington Post journalist Bob Woodward's forthcoming book, "Fear," which contains dozens of vignettes and quotes from current and former Trump officials that paint the president in a startlingly negative light.