Pirro's office, in a court filing on Friday, moved to drop criminal charges against a former Olympian, David Hearn, who had been accused of deliberately damaging the pool after it underwent a renovation ahead of the nation's 250th birthday celebration last month.
Trump, in a posting on social media, acknowledged that there "may have been some contractor difficulty" in the installation of a new pool liner. But he continues to insist "the major damage was caused by VANDALS!"
"I disagree 100% with Jeanine Pirro, the US Attorney for the District of Columbia, on the Reflecting Pool," Trump added in his post.
The dismissal was an embarrassing setback for a Justice Department that had previously echoed Trump's claims and billed the prosecution as accountability for damage at a Washington landmark, a pet project of Trump.
Pirro's decision to drop the case is also a rare moment during Trump's second term of an aide or political appointee openly defying him.
The president continued to allege on Saturday that the majority of the damage to the pool was caused by vandals.
Government lawyers in their 20-page court filing on Friday said that additional documents provided by the Interior Department since the indictment of Hearn show that the damage was the result of a botched installation by a contractor as well as "the rush to complete the project prior to events associated with the America 250 celebration in the weeks surrounding Independence Day 2026".
In addition, a recent visual inspection revealed damage throughout the pool, including in the middle - where prosecutors say a vandal would not likely have attempted to peel the lining.
Hearn, a former Olympic canoeist, was accused of pulling up a piece of the pool's lining.
"Given all of this newly discovered information, it is difficult to attribute the widespread damage to the Reflecting Pool to vandalism, let alone to establish that fact beyond a reasonable doubt," Pirro, a Trump appointee, said in her filing, which asked a judge to formally dismiss the case.
Pirro in the court filing also blamed the Interior Department for providing "less than fulsome information at the outset of the case".
The filing added that had "DOI been forthcoming with the information clearly in its possession, the government would not have sought a grand jury indictment".
It was a jarring turn in position from Pirro, who claimed the government's case was built on "tremendous evidence" when she announced the indictment against Hearn in July.
Hearn's legal team said it was weighing "legal remedies" on behalf of their client.
"Trump is mad at Pirro because she finally admitted what we made clear in our legal filings all along: Trump's botched renovation was responsible for the damage - not Davey Hearn," the legal team said in a statement.
In May, Trump announced plans to beautify the Reflecting Pool.
Atlantic Industrial Coatings was awarded a $US14.7 million ($A21 million) no-bid contract to repaint and waterproof the pool's concrete floor.
