"We're in foreign territory," Bernstein said Friday on CNN's "New Day."
He added, "We have never been in a malignant presidency like this before. It calls on our leaders, it calls on our journalists to do a different kind of reporting, a different kind of dealing with this presidency and the president."
Bernstein, best known for his investigative reporting that shed light on the Watergate scandal leading to President Richard Nixon's resignation in 1974, has previously said Trump's attacks on the press are "more treacherous than Nixon's."
Recently Trump has ramped up his criticism of certain outlets and journalists, including MSNBC's Joe Scarborough and Mika Brzezinski. On Saturday he continued that feud and also took shots at MSNBC and CNN.
"I think something much greater is happening, and that is that we are in the midst of a malignant presidency," Bernstein said Friday. He added that leaders in the military, intelligence community and the Republican leadership know of the "malignancy" and has them "worried."
"They are worried about his character. They are worried about his capabilities. They are worried about his temperament and state of his temperament, to use kind words here," he said.