The diagnosis of a “deep state,” those experts say, has the problem backward.

Mr. Trump has put institutions under enormous stress. He has attacked them publicly, implied he would reject intelligence findings that cast his election in a poor light, hobbled agencies by failing to fill critical positions and cut off bodies like the National Security Council from shaping policy.

That has forced civil servants into an impossible dilemma: acquiesce, allowing their institution to be sidelined, or mount a defense, for example through leaks that counter Mr. Trump’s accusations or pressure him into restoring normal policy-maker practices.

Those defensive acts have deepened perceptions in the Trump administration of a “deep state” that must be rooted out. This tit-for-tat cycle, scholars say, risks substantially weakening both Mr. Trump and government institutions. In the long term, they warn, this could undermine the government’s ability to function — and to serve the millions of Americans who depend on it.