“In all my time at @Twitter, I’m not sure I’ve ever seen folks so energetic, enthusiastic, & ready to collaborate as after #OneTeam,” Del Harvey, the head of Twitter’s trust and safety team, tweeted at the time.

Then late on Sunday, Apple yanked most of the content from Mr. Jones and Infowars off its iTunes store, quickly followed by deletions at Facebook, YouTube, and Spotify. At Twitter, executives met on Monday morning to debate their own response. They ultimately decided that Mr. Jones had not committed enough infractions to result in a permanent ban from the site.

Mr. Dorsey discussed that decision on Tuesday in an internal post on Periscope, the live-streaming video platform owned by Twitter, according to an employee who watched the stream and who was not authorized to speak publicly.

Yet Twitter publicly kept silent about its process, drawing a barrage of criticism from users who said the site was protecting Mr. Jones and Infowars. Mr. Jones later went on Twitter to blast other social media companies for what he said was their censorship, and called on President Trump to weigh in on the takedowns.

Mr. Jones did not respond to a request for comment.

On Tuesday evening, Mr. Dorsey finally posted about Twitter’s decision to keep up the posts of Infowars and Mr. Jones. In his tweets, the chief executive suggested that other social media companies had caved to political pressure by removing Mr. Jones’s content. He also said the task of fact-checking Mr. Jones’s sensational claims should fall to journalists on the platform rather than Twitter’s own moderators, prompting confusion.

Emily Horne, a former Twitter spokeswoman, lashed out at Mr. Dorsey for blaming the communications staff for failing to adequately explain rules. “These decisions aren’t easy, but they aren’t comms calls and it’s unhelpful to denigrate your colleagues,” Ms. Horne tweeted, adding that leaving up Mr. Jones’s posts was “the wrong call.”