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The account was down for 11 minutes before it was restored, the social media company said.
Trump has 41.7 million followers on Twitter and has made extensive use of it to send messages attacking his opponents and promoting his policies, both during the 2016 presidential campaign and since taking office in January.
"We have learned that this was done by a Twitter customer-support employee who did this on the employee's last day. We are conducting a full internal review," Twitter said in a tweet.
"We are continuing to investigate and are taking steps to prevent this from happening again," the company said in an earlier tweet.
A Twitter representative declined to comment further.
The White House did not immediately respond to a request for comment.
In his first tweet after Thursday's outage, Trump wrote, "Great Tax Cut rollout today. The lobbyists are storming Capital Hill, but the Republicans will hold strong and do what is right for America!"
Thursday evening's incident raises a host of questions about how Twitter secures Trump's personal account, the official @potus presidential account and other accounts that could potentially influence world events.
It comes at a moment when technology companies, including Twitter, face sharp attack from US lawmakers for failing to stem the spread of Russian propaganda and misinformation on their platforms.
Twitter, in particular, has long faced criticism for not doing enough to police its platform and respond to complaints of abuse.
The temporary deletion of the Trump account sparked a flood of criticism on Twitter itself. Reuters could not determine how many Twitter employees had the authority to delete accounts or tamper with them in in other ways, such as by sending counterfeit Tweets.
Twitter declined to provide further details