The sudden suspension of news reporters from, among others, The New York Times, Washington Post and CNN, comes after Mr Musk accused journalists of sharing private information about his real-time location, which he described as "basically assassination coordinates.”
The data used to track his private jet - Elon Jet - is publically available.
In response to his accusation, Twitter changed its rules to ban all users from sharing another person’s current location without their consent.
Several of the reporters suspended on Thursday night had been writing about that new policy and the possible reasons behind Mr Musk's decision, which involved his allegations about a stalking incident he said affected his family on Tuesday night in Los Angeles.
Journalists say banning accounts contradicts Mr Musk's vocal commitment to free speech.
“Same doxxing rules apply to ‘journalists’ as to everyone else," Musk tweeted on Thursday.
He later added: “Criticizing me all day long is totally fine, but doxxing my real-time location and endangering my family is not.”
“Doxxing” refers to disclosing online someone’s identity, address, or other personal details.
The Washington Post’s executive editor, Sally Buzbee, called for technology reporter Drew Harwell’s Twitter account to be reinstated immediately.
The suspension “directly undermines Elon Musk’s claim that he intends to run Twitter as a platform dedicated to free speech,” Buzbee wrote.
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“Harwell was banished without warning, process or explanation, following the publication of his accurate reporting about Musk.”
CNN said in a statement that “the impulsive and unjustified suspension of a number of reporters, including CNN’s Donie O’Sullivan, is concerning but not surprising.”
“Twitter’s increasing instability and volatility should be of incredible concern for everyone who uses Twitter,” CNN's statement added.
“We have asked Twitter for an explanation, and we will reevaluate our relationship based on that response.”
Late on Thursday, Mr Musk briefly joined a Twitter Spaces conference chat hosted by journalist Kate Notopoulos of Buzzfeed.
He reiterated his claims that the banned journalists were “doxxing" him when they were reporting on the jet tracking accounts being banned.
“There is not special treatment for journalists,” Musk said, after being asked by the Post’s Drew Harwell if he had a connection between the stalking incident and posting of real-time information.
“You dox, you get suspended, end of story,” he added, before abruptly signing out.
The suspensions come as Mr Musk makes major changes to content moderation on Twitter. He has tried, through the release of selected company documents dubbed as “The Twitter Files,” to claim the platform suppressed right-wing voices under its previous leaders.
He has promised to let free speech reign and has reinstated high-profile accounts, including former US president Donald Trump, that previously broke Twitter's rules against hateful conduct or harmful misinformation, but also has said he would suppress negativity and hate by depriving some accounts of “freedom of reach.”