Some concerns arose even before the Stone situation. In the past two weeks, the Justice Department has twice ordered US attorney's offices around the country to participate in what some of them perceive as politically charged actions, according to people familiar with the matter.

First, the department ordered prosecutors to hold news conferences, make statements and use social media to promote Barr's initiative to crack down on "sanctuary cities," according to a person with direct knowledge of the matter. The Justice Department later retracted the demand, the person said. Still, at least two US attorneys wrote op-eds.

The department also instructed federal prosecutors to write op-eds to push for passage of pending legislation on fentanyl. More than a dozen US attorneys complied with publishing op-eds or written statements. The person said that historically prosecutors have been instructed to avoid commenting on pending legislation.