A federal judge on Monday declared the Trump administration’s move to cut hundreds of grants issued by the National Institutes of Health illegal, accusing the government of discrimination against minorities and L.G.B.T.Q. individuals.

Ruling from the bench, Judge William G. Young of the Federal District Court for the District of Massachusetts ordered the government to restore much of the funding.

Judge Young, a Reagan appointee with 40 years of experience as a federal judge, said the Trump administration’s rationale for canceling the grants, which support research into topics such as gender identity and equity in health care, appeared to be rooted in prejudice. He noted the administration’s efforts to eliminate any trace of diversity and equity initiatives from the federal government, as well as its attacks on transgender people.

He said that throughout his career he had “never seen government racial discrimination like this,” and that he felt duty bound to state his conclusion about the government’s intent.

“I would be blind not to call it out,” he said.

Judge Young’s ruling echoed arguments during a brief trial earlier in the day in which lawyers from an array of groups said the grants had become a political target.

Kenneth Parreno, a lawyer representing the American Public Health Association, called the government’s actions part of a campaign to ban “forbidden topics” in science by canceling grants related to race or transgender health.

“What this is, is a slapdash, harried effort to rubber stamp an ideological purge,” he said.

The Trump administration in March began terminating a number of public health grants supporting research on topics such as health equity, racial disparities, vaccine hesitancy, and maternal health in minority communities, sometimes by mechanically scanning for certain terms.

In May, Mr. Trump signed an order called “Restoring Gold Standard Science” that cited a “reproducibility crisis” and resurrected policy disputes from the Covid-19 pandemic, among other things, as justification for deep changes to the government’s role in research and development.

In two separate cases that were heard together, a coalition of Democratic-led states and a coalition of unions, researchers and public health organizations each sued to stop a raft of cuts at the N.I.H., which they said jeopardized scientific progress.

In hearings leading up to the ruling on Monday, Judge Young repeatedly pressed for details about the government’s decision making, expressing deep skepticism that it had followed normal, dispassionate processes in terminating the grants.