Former FBI Director James Comey was “troubled” by then-Attorney General Loret­ta Lynch’s “pro-Clinton bias” at the beginning of the Hillary Clinton email probe, a bombshell new book claims.

Comey was “nagged in his distrust of Lynch’s impartiality” after he received a report from a “highly placed informant” in March 2016 suggesting the AG was trying to nix the investigation, reporter James B. Stewart claims in his new book “Deep State: Trump, the FBI and the Rule of Law,” released Tuesday.

The document contained an email that Deborah Wasserman Schultz, then-chair of the Democratic National Committee, reportedly sent to an executive at Open Society Foundations, founded by billionaire Democratic donor George Soros, Stewart wrote.

The email assured executive Leonard Benardo that “Lynch wouldn’t let the Clinton investigation get very far, suggesting that Lynch would protect Clinton,” Stewart wrote.

But both Wasserman and Benardo have denied the email exists — telling the Washington Post they have never met or communicated with each other

Comey began having lingering suspicions about Lynch’s Department of Justice after the FBI in July 2015 opened a criminal investigation into Clinton’s use of her private email server while secretary of state, Stewart wrote.

At a September 2015 meeting between Comey and Lynch, the FBI chief reportedly felt “queasy” and “troubled” when Lynch pressured him not to call the probe an investigation but “a matter” — aligning with Clinton’s presidential campaign’s contention at the time that there was no investigation, Stewart wrote.

“That concerned me because that language tracked the way the campaign was talking about the FBI’s work, and that’s concerning,” Comey told the Senate Intelligence Committee in June 2017.

The book also details how a “tone-deaf” Bill Clinton ambushed Lynch in a secret meeting on her private DOJ plane at Sky Harbor Airport in Phoenix in June 2016.

According to Stewart, the ex-president forced an uneasy Lynch into a 20-minute private conversation with him as she was about to get off the plane with her husband and staff for an official visit.

“That Lynch thought she could escape an encounter with Bill Clinton with a handshake and a few pleasantries confirmed the fact that she barely knew the garrulous former president,” Stewart wrote, claiming Clinton waffled about his grandchildren, the Arizona heat and his golf game — oblivious to the fact no one wanted him there and Lynch had turned “gray.”

Her staff was “furious that Lynch’s FBI security guard let Clinton on the plane,” Stewart wrote, and were “astonished” that Clinton would be “so tone-deaf as to initiate an extended private conversation with the AG, the very person weighing criminal charges against his wife.”

Lynch did not respond to a request for comment.