Conflict between the state and federal government began after President Donald Trump issued the order titled "Defending Women from Gender Ideology Extremism and Restoring Biological Truth to the Federal Government" on his first day back in the White House for a second term.

The Epoch Times' Travis Gillmore reports that in a 70-page ruling, Judge John A. Woodcock Jr. ordered the Department of Agriculture and its secretary, Brooke Rollins, to "immediately unfreeze" any money held back because the state chose not to follow the president's executive action.

Agencies are also barred from withholding future funding on similar grounds.

Meanwhile, the court distanced itself from the debate over transgender athletes.

"In ruling on the state's request, the court is not weighing in on the merits of the controversy about transgender athletes that forms the backdrop of the impasse between the state and the federal defendants," Woodcock wrote in his decision.

He went on to explain that the decision was based on the Agriculture Department's failure to follow regulatory protocols when withholding the funding.

"In fact, the federal defendants have not argued in this case that the relevant federal laws and regulations for terminating federal funding of state programs do not apply to this situation, nor do they claim that they complied with the applicable federal law in the events resulting in this litigation."

The Trump administration argued that the court did not have proper jurisdiction to hear the case, and that Maine did not "allege irreparable harm."

Tensions boiled over during a February meeting with governors at the White House, when Trump and Maine Gov. Janet Mills sparred over the issue in a heated back-and-forth.

When Maine opted not to prohibit transgender athletes from competing against women, Rollins sent a letter April 2 to Mills alerting her that the Agriculture Department was "freezing Maine's federal funds for certain administrative and technological functions in schools," according to the court ruling.

In its lawsuit filed on April 7, Maine said it was unable to access approximately $3 million.

The state told the court the money was used for programs that helped provide meals to schools, childcare facilities, and disabled adults.