Later, Twitter restored the tweet, saying an "outage" was behind the disappearance of Trump's tweet.
"Due to an outage with one of our systems, tweets on account profiles were visible to some, but not others. We're still working on fixing this and apologize for any confusion," the company said in a statement on Sunday.
However, the statement did not bode well for most users.
"I find this all very odd. To you, you think there is no issue as you can see it. But to others your tweet has disappeared. This really is most odd. Mostly on Trump tweets?" a user responded to Twitter Safety.
Some tech companies, including YouTube and Facebook, have blocked the alleged whistleblower's name from appearing on its platforms.
Twitter, however, has said that naming the individual would not violate the company's policies.
"Why does it always happen to republican or Trump supporter accounts...very unusual for just an 'outage' seems an outage would affect everyone across the spectrum...," another user posted.
President Trump came under fire after retweeting a post to his followers on Twitter that included a name linked to the alleged whistleblower.
"By making public the unsubstantiated name of the whistleblower Trump encapsulated the pathology of his presidency," Aaron David Miller, senior fellow at the Carnegie Endowment and former State Department analyst, was quoted as saying in an NPR report.
"A callous and cruel disregard for the well-being of anyone one or anything untethered from his own personal needs and interests."
( With inputs from IANS )