In the years after President Richard Nixon enlisted the Internal Revenue Service to investigate his political opponents, Congress passed a series of laws to make sure the agency would focus on collecting taxes and not use its vast powers to carry out political vendettas.

But President Trump has moved swiftly to suppress that independence in the first few months of his second term and, tax experts and former agency officials warn, return the I.R.S. to darker days when it was used as a political tool of the president.

His administration has decimated the ranks of I.R.S. civil servants and moved to install political allies in their place. This week, he publicly called for Harvard to lose its tax-exempt status, an extraordinary attempt to enlist the I.R.S. in his feud with the wealthy research university. In the Oval Office on Thursday, Mr. Trump renewed that threat and suggested that several other universities the administration has accused of antisemitism could also lose their tax-exempt status.

“Tax-exempt status, it’s a privilege, it’s really a privilege and it’s been abused by a lot more than Harvard, so we’ll see how that all works out,” he said, also mentioning Columbia and Princeton.

The I.R.S. is now weighing whether to revoke Harvard’s tax exemption, as The New York Times reported earlier this week.

Federal law bars the president from ordering the I.R.S. to conduct specific tax investigations. A White House spokesman has said the agency’s scrutiny of Harvard began before the president’s social media post. Mr. Trump said Thursday that he did not believe the I.R.S. had “made a final ruling.”