The former special counsel, Robert S. Mueller III, rebutted allegations on Tuesday from one of the top prosecutors in his office that his team could have more aggressively scrutinized President Trump’s ties to Russia and could have called out his efforts to obstruct the investigation.
The former top prosecutor, Andrew Weissmann, said in a new book that Mr. Mueller and some members of his team were cowed by the president’s threats to fire them. The book, “Where Law Ends,” was released on Tuesday and provided the first insider account of the special counsel’s investigation.
In a rare public statement, Mr. Mueller said that Mr. Weissmann lacked a full picture of decision-making on the team and cast his critiques as typical disagreements among prosecutors in any high-profile investigation.
“It is not surprising that members of the special counsel’s office did not always agree, but it is disappointing to hear criticism of our team based on incomplete information,” Mr. Mueller said.
Mr. Weissmann declined to comment.
The disclosures by Mr. Weissmann in his book renewed criticisms that Mr. Mueller fell short in his investigation, including by failing to scrutinize Mr. Trump’s finances or taking a position on whether Mr. Trump illegally obstructed justice.
Attorney General William P. Barr has also taken steps to undermine Mr. Mueller’s work, including releasing a summary of the Mueller report before the public could read it that a judge later called distorted and misleading, and intervening in two of the special counsel’s office’s most prominent investigations.
One of Mr. Weissmann’s chief criticisms was aimed at Mr. Mueller’s deputy, Aaron M. Zebley, who Mr. Weissmann described as too reluctant to take on Mr. Trump and constantly getting in the way of efforts to uncover a deeper understanding of what occurred between Mr. Trump, his 2016 campaign and Russia.
“Repeatedly during our 22 months in operation, we would reach some critical juncture in our investigation only to have Aaron say that we could not take a particular action because it risked aggravating the president beyond some undefined breaking point,” Mr. Weissmann wrote.
In one passage, Mr. Weissmann asserted that Mr. Zebley had agreed, without consulting with Mr. Mueller, to a request by the Justice Department to not share the team’s evidence with state prosecutors, lest that undermine Mr. Trump’s pardon power. (Two former officials have disputed whether there was such a commitment.)
Mr. Mueller declined to address the specifics in Mr. Weissmann’s book but said that he had the final say in major decisions and defended Mr. Zebley, his former chief of staff when Mr. Mueller was director of the F.B.I.
“My deputy, Aaron Zebley, was privy to the full scope of the investigation and all that was at issue,” Mr. Mueller said. “I selected him for that role because I knew from our 10 years working together that he is meticulous and principled. He was an invaluable and trusted counselor to me from start to finish.”
“When important decisions had to be made, I made them,” Mr. Mueller said. “I did so as I have always done, without any interest in currying favor or fear of the consequences. I stand by those decisions and by the conclusions of our investigation.”
Mr. Weissmann was also critical of Mr. Mueller’s decision to not subpoena the president for testimony.
“We would have subpoenaed the president after he refused our accommodations, even if that risked us being fired,” Mr. Weissmann wrote. “It just didn’t sit right. We were left feeling like we had let down the American public, who were counting on us to give it our all.”
Mr. Mueller acknowledged that his decisions were certain to be widely criticized.
“The office’s mission was to follow the facts and to act with integrity,” Mr. Mueller said. “That is what we did, knowing that our work would be scrutinized from all sides.”
Mr. Mueller did not speak publicly during the investigation and has only done so a handful of times since it ended.
In May, Mr. Barr asked a federal judge to throw out the case made by the special counsel’s office against Mr. Trump’s first national security adviser, Michael T. Flynn. In July, Mr. Trump commuted the sentence of his longtime adviser, Roger J. Stone Jr., who Mr. Mueller’s office had indicted on lying to Congress about whether he had served as a conduit between Mr. Trump’s campaign and WikiLeaks, which disseminated Democratic emails stolen by Russian agents during the 2016 election.
The day after the commutation Mr. Mueller published an opinion piece in The Washington Post defending the case against Mr. Stone, saying “he remains a convicted felon, and rightly so.”