It said Trump received the equivalent of $413 million in today's dollars from his father's real estate activities.
"The New York Times' allegations of fraud and tax evasion are 100 percent false, and highly defamatory", Harder said, according to the paper.
The host noted that one of the largest revelations from the Times report was the previously-unknown existence of All County Building Supply & Maintenance, a shell company the patriarch used to markup appliances used in his buildings and reap the benefits so he could give large, tax-exempt monetary gifts to his kids. It says that the president's parents had transferred wealth worth over $1 billion to their children which would evoke a tax bill of at least $550 million under the then existing 55 percent tax rate on gifts and inheritances.
But the newspaper said its exhaustive investigation of a vast trove of tax returns and confidential records found this was not true. "The facts upon which The Times bases its false allegations are extremely inaccurate", the statement continued.
It also renews questions about what may be lurking in the tax returns Trump kept private as he ran for and assumed the presidency in January 2017. The White House earlier referred questions to Charles Harder, a private attorney for Trump.
The New York Times claimed that Mr Trump helped his parents "dodge" taxes and undervalue property which reduced the tax bill.
Harder added: "The affairs were handled by other Trump family members who were not experts themselves and therefore relied entirely upon the aforementioned licensed professionals to ensure full compliance with the law".
For example, the Times said Fred Trump gave ownership of most of his real estate empire to his children a year and a half before his death.
"The Tax Department is reviewing the allegations in the NYT article and is vigorously pursuing all appropriate avenues of investigation", a spokesman from the New York State Department of Taxation and Finance said in an email, the news outlet reported.
"The Times calls this scheme around this company the most overt in Trump's company", Maddow said, later noting that the appliance markups were a fairly simple example of "tax evasion". Those statements do not indicate who the buyer of the stake was, but other records - including an affidavit from Donald Trump - show that it was sold to his son.
The New York Times reported that the president is unlikely to face criminal investigation as the alleged events happened too long ago.
The report, which could potentially explain why Trump has resolutely refused to release his tax returns, has reportedly caught the notice of investigators from NY, where the Trump Organization is headquartered.