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An employee deactivated the@realdonaldtrump account, it said, clarifying that it had been their last day in the job.
The account was down for 11 minutes and Twitter is now investigating.
Tweets from Mr Trump, who has 41.7 million followers, have frequently caused controversy.
The latest incident has sparked debate about the security of the president's account, given the potential consequences of posts falsely attributed to Mr Trump being published.
However, @POTUS, the official account of the US president, was unaffected.
'Last day'
On Thursday evening, visitors to Mr Trump's page for a short time could only see a message that read "Sorry, that page doesn't exist!"
Image copyrightTWITTER
Image captionDonald Trump has been actively using Twitter to promote his policies and attack his opponents
After the account was restored, Mr Trump's first tweet was about the Republican Party's tax cuts plan.
Twitter said it was investigating the problem and taking steps to avoid it happening again.
It later said: "Through our investigation 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."
End of Twitter post by @realDonaldTrump
It said that Mr Trump's tweet was "newsworthy".
In some of his other most controversial tweets:
Mr Trump's allies have also got into hot water over their use of Twitter.
Roger Stone, who advised him during his election campaign, was suspended from the network after he used abusive and homophobic language to target journalists, including a gay CNN presenter, Don Lemon.
He said he had been told by Twitter that he had violated its rules.
Mr Stone said he would sue Twitter for blocking his account.
